Publications by authors named "Jizhong Zhou"

482 Publications

Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches.

mBio 2021 04 20;12(2). Epub 2021 Apr 20.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA

Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, , growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches. Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.03509-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092305PMC
April 2021

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.

Front Microbiol 2021 24;12:642422. Epub 2021 Mar 24.

Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.642422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8024649PMC
March 2021

Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network.

Research (Wash D C) 2021 10;2021:7102769. Epub 2021 Mar 10.

Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.

Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.34133/2021/7102769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7978035PMC
March 2021

Author Correction: Temporal changes in global soil respiration since 1987.

Nat Commun 2021 Mar 16;12(1):1801. Epub 2021 Mar 16.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-22014-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7966743PMC
March 2021

Microbial Functional Responses Explain Alpine Soil Carbon Fluxes under Future Climate Scenarios.

mBio 2021 02 23;12(1). Epub 2021 Feb 23.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China

Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO and CH fluxes across all sites significantly (>0.70, < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities. The warming pace in the Tibetan Plateau, which is predominantly occupied by grassland ecosystems, has been 0.2°C per decade in recent years, dwarfing the rate of global warming by a factor of 2. Many Earth system models project substantial carbon sequestration in Tibet, which has been observed. Here, we analyzed microbial communities under projected climate changes by 2100. As the soil "carbon pump," the growth and activity of microorganisms can largely influence soil carbon dynamics. However, microbial gene response to future climate scenarios is still obscure. We showed that the abundances of microbial functional genes, but not microbial taxonomy, were correlated with carbon fluxes and ecosystem multifunctionality. By identifying microbial traits linking to ecosystem functioning, our results can guide the assessment of future soil carbon fluxes in alpine grasslands, a critical step toward mitigating climate changes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00761-20DOI Listing
February 2021

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions.

ISME J 2021 Feb 21. Epub 2021 Feb 21.

Institute for Systems Biology, Seattle, WA, 98109, USA.

Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-021-00919-9DOI Listing
February 2021

Rare prokaryotic sub-communities dominate the complexity of ecological networks and soil multinutrient cycling during long-term secondary succession in China's Loess Plateau.

Sci Total Environ 2021 Jun 9;774:145737. Epub 2021 Feb 9.

State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address:

Unraveling the succession of microbial communities is a core ecological research topic. Yet few studies have focused on how long-term secondary succession affects the functional profiles and ecological processes of abundant and rare microbial subcommunities. Here, we used amplicon sequencing and GeoChip analysis to explore the ecological functions of abundant and rare biospheres and their correlation with soil multinutrient cycling. Samples for this study were collected from a well-established secondary succession chronosequence that spans >30 years of dryland ecosystem development on the Loess Plateau of China. Although both abundant and rare subcommunities shifted with succession, the changing of beta-diversity of the microbial communities was primarily driven by species replacement of the rare biosphere. Phylogenetic changes of abundant and rare taxa were associated with their functional traits, which dominated the diversity-related selection along all succession ages. Neutral theory analysis indicated that the assemblage of abundant taxa over all successional ages was regulated by dispersal homogenizing and ecological drift. The null model revealed that homogeneous and variable selection were the dominant assembly processes for rare subcommunities compared with abundant species. pH and nitrogen content were the paramount drivers determining the assembly of microbial communities and functional genes, consistent with the importance of environmental filtering. Furthermore, the rare biosphere had a paramount role in the entire ecological network and was the major driver for most soil processes such as C, N, and S cycling. Nonetheless, a significant portion of soil P cycling was regulated by abundant taxa. Collectively, our study provides insight into the mechanisms underlying microbial community assembly and soil microbe-driven functional changes in biogeochemical processes during secondary succession.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2021.145737DOI Listing
June 2021

Edaphic variables are better indicators of soil microbial functional structure than plant-related ones in subtropical broad-leaved forests.

Sci Total Environ 2021 Jun 6;773:145630. Epub 2021 Feb 6.

Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China. Electronic address:

Soil microorganisms play important roles in the ecosystem functioning of subtropical broad-leaved forests (SBFs). However, the patterns and environmental indicators of soil microbial functional structure remain unclear in SBFs. In the present work, we used a functional microarray (GeoChip 4.0) to examine the soil microbial functional structure of three types of SBFs, including a deciduous broad-leaved forest (DBF), a mixed evergreen-deciduous broad-leaved forest (MBF), and an evergreen broad-leaved forest (EBF). We found that microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher functional α-diversity (P = 0.001, F = 12.55) but lower β-diversity (P < 0.001, F = 61.09), and showed more complex functional gene networks. Besides, the MBF had higher relative abundances of functional genes for carbon (C) decomposition, C fixation, nitrogen (N) cycling, sulfur (S) cycling, and phosphorus (P) cycling (P < 0.05), indicating stronger microbial functional capabilities of nutrient cycling processes. Edaphic variables (i.e., soil pH and soil nutrient content) were revealed as better indicators of soil microbial functional structure than plant-related ones (i.e., vegetation type and plant diversity) in SBFs. For example, functional gene structure of the DBF was significantly related to soil total S (P = 0.041), that of the MBF was significantly related to soil organic C (P = 0.027) and plant available P (P = 0.034), and that of the EBF was significantly related to soil pH (P = 0.006) and total potassium (K) (P = 0.038). Overall, through the analysis of microbial functional gene profiles, this study yields unique insights into the environmental indicators of patterns and mechanisms of soil microbial functional structure in SBFs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2021.145630DOI Listing
June 2021

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition.

NPJ Biofilms Microbiomes 2021 02 8;7(1):17. Epub 2021 Feb 8.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.

Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8-1.0 °C for 10 years and then 1.5-2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41522-021-00187-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7870951PMC
February 2021

Microbial metabolic response to winter warming stabilizes soil carbon.

Glob Chang Biol 2021 May 13;27(10):2011-2028. Epub 2021 Feb 13.

Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.

Current consensus on global climate change predicts warming trends with more pronounced temperature changes in winter than summer in the Northern Hemisphere at high latitudes. Moderate increases in soil temperature are generally related to faster rates of soil organic carbon (SOC) decomposition in Northern ecosystems, but there is evidence that SOC stocks have remained remarkably stable or even increased on the Tibetan Plateau under these conditions. This intriguing observation points to altered soil microbial mediation of carbon-cycling feedbacks in this region that might be related to seasonal warming. This study investigated the unexplained SOC stabilization observed on the Tibetan Plateau by quantifying microbial responses to experimental seasonal warming in a typical alpine meadow. Ecosystem respiration was reduced by 17%-38% under winter warming compared with year-round warming or no warming and coincided with decreased abundances of fungi and functional genes that control labile and stable organic carbon decomposition. Compared with year-round warming, winter warming slowed macroaggregate turnover rates by 1.6 times, increased fine intra-aggregate particulate organic matter content by 75%, and increased carbon stabilized in microaggregates within stable macroaggregates by 56%. Larger bacterial "necromass" (amino sugars) concentrations in soil under winter warming coincided with a 12% increase in carboxyl-C. These results indicate the enhanced physical preservation of SOC under winter warming and emphasize the role of soil microorganisms in aggregate life cycles. In summary, the divergent responses of SOC persistence in soils exposed to winter warming compared to year-round warming are explained by the slowing of microbial decomposition but increasing physical protection of microbially derived organic compounds. Consequently, the soil microbial response to winter warming on the Tibetan Plateau may cause negative feedbacks to global climate change and should be considered in Earth system models.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/gcb.15538DOI Listing
May 2021

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

Microbiome 2021 01 22;9(1):20. Epub 2021 Jan 22.

State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.

Background: Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks.

Results: The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa.

Conclusions: These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-020-00978-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825242PMC
January 2021

The call for regional design code from the regional discrepancy of microbial communities in activated sludge.

Environ Pollut 2021 Jan 12;273:116487. Epub 2021 Jan 12.

Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, PR China. Electronic address:

Discerning the differences in activated sludge (AS) microbial community due to geographic location and environmental and operational factors is of great significance for precise design and maintenance of wastewater treatment plants (WWTPs). Hence, in this study, 150 AS samples collected from WWTPs in South China and North China were analyzed by 16 S rRNA gene sequencing. In general, AS microbial community in North China had lower diversity, higher proportions of stochastic assembly (35.7% v.s. 15.8%) and more network keystone species (19 v.s. 5) compared with southern AS community. Conductivity and SRT had significant effects on AS community in both regions. Latitude, annual mean temperature, and influent BOD, COD, and ammonia influenced South China community significantly, while pH and influent total phosphorus affected North China community. To achieve stable performance, southern WWTPs should carefully monitor fluctuations in wastewater characteristics, while northern WWTPs should monitor AS communities for shifts in the dominant taxa from immigrant strains brought in through the influent. Additionally, WWTPs in North China should be aware of the need to proactively control sludge bulking because of the high abundance and occurrence of Haliscomenobacter in these AS communities. MAIN FINDING: The call for regional design based on the regional discrepancy of microbial communities in activated sludge is uncovered and according suggestions were given.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envpol.2021.116487DOI Listing
January 2021

Temporal changes in global soil respiration since 1987.

Nat Commun 2021 01 15;12(1):403. Epub 2021 Jan 15.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.

As the second-largest terrestrial carbon (C) flux, soil respiration (R) has been stimulated by climate warming. However, the magnitude and dynamics of such stimulations of soil respiration are highly uncertain at the global scale, undermining our confidence in future climate projections. Here, we present an analysis of global R observations from 1987-2016. R increased (P < 0.001) at a rate of 27.66 g C m yr (equivalent to 0.161 Pg C yr) in 1987-1999 globally but became unchanged in 2000-2016, which were related to complex temporal variations of temperature anomalies and soil C stocks. However, global heterotrophic respiration (R) derived from microbial decomposition of soil C increased in 1987-2016 (P < 0.001), suggesting accumulated soil C losses. Given the warmest years on records after 2015, our modeling analysis shows a possible resuscitation of global R rise. This study of naturally occurring shifts in R over recent decades has provided invaluable insights for designing more effective policies addressing future climate challenges.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-20616-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810831PMC
January 2021

Stimulation of soil respiration by elevated CO is enhanced under nitrogen limitation in a decade-long grassland study.

Proc Natl Acad Sci U S A 2020 12 14;117(52):33317-33324. Epub 2020 Dec 14.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084 Beijing, China;

Whether and how CO and nitrogen (N) availability interact to influence carbon (C) cycling processes such as soil respiration remains a question of considerable uncertainty in projecting future C-climate feedbacks, which are strongly influenced by multiple global change drivers, including elevated atmospheric CO concentrations (eCO) and increased N deposition. However, because decades of research on the responses of ecosystems to eCO and N enrichment have been done largely independently, their interactive effects on soil respiratory CO efflux remain unresolved. Here, we show that in a multifactor free-air CO enrichment experiment, BioCON (Biodiversity, CO, and N deposition) in Minnesota, the positive response of soil respiration to eCO gradually strengthened at ambient (low) N supply but not enriched (high) N supply for the 12-y experimental period from 1998 to 2009. In contrast to earlier years, eCO stimulated soil respiration twice as much at low than at high N supply from 2006 to 2009. In parallel, microbial C degradation genes were significantly boosted by eCO at low but not high N supply. Incorporating those functional genes into a coupled C-N ecosystem model reduced model parameter uncertainty and improved the projections of the effects of different CO and N levels on soil respiration. If our observed results generalize to other ecosystems, they imply widely positive effects of eCO on soil respiration even in infertile systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2002780117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7777058PMC
December 2020

Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.

Mol Ecol 2021 02 22;30(4):926-937. Epub 2020 Dec 22.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.

High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2°C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.15773DOI Listing
February 2021

Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism.

Environ Microbiol 2021 02 8;23(2):1199-1209. Epub 2021 Feb 8.

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.

Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N-cycling-microbes within different soil particle-size fractions under a long-term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N O production and reduction of the microbial communities attached to different sized soil particles (2000-250, 250-53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N O production and reduction rates were greater in 2000-250 and 250-53 μm across different fertilizer regimes. The abundance of key N-cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N -fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N-cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N-cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.15348DOI Listing
February 2021

The microbial network property as a bio-indicator of antibiotic transmission in the environment.

Sci Total Environ 2021 Mar 14;758:143712. Epub 2020 Nov 14.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China. Electronic address:

Interspecies interaction is an essential mechanism for bacterial communities to develop antibiotic resistance via horizontal gene transfer. Nonetheless, how bacterial interactions vary along the environmental transmission of antibiotics and the underpinnings remain unclear. To address it, we explore potential microbial associations by analyzing bacterial networks generated from 16S rRNA gene sequences and functional networks containing a large number of antibiotic-resistance genes (ARGs). Antibiotic concentration decreased by more than 4000-fold along the environmental transmission chain from manure samples of swine farms to aerobic compost, compost-amended agricultural soils, and neighboring agricultural soils. Both bacterial and functional networks became larger in nodes and links with decreasing antibiotic concentrations, likely resulting from lower antibiotics stress. Nonetheless, bacterial networks became less clustered with decreasing antibiotic concentrations, while functional networks became more clustered. Modularity, a key topological property that enhances system resilience to antibiotic stress, remained high for functional networks, but the modularity values of bacterial networks were the lowest when antibiotic concentrations were intermediate. To explain it, we identified a clear shift from deterministic processes, particularly variable selection, to stochastic processes at intermediate antibiotic concentrations as the dominant mechanism in shaping bacterial communities. Collectively, our results revealed microbial network dynamics and suggest that the modularity value of association networks could serve as an important indicator of antibiotic concentrations in the environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.143712DOI Listing
March 2021

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe.

Sci Total Environ 2021 Apr 9;764:142848. Epub 2020 Oct 9.

CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha year) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha year was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha year) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha year) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO/NH and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.142848DOI Listing
April 2021

Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4.

Appl Environ Microbiol 2021 01 4;87(2). Epub 2021 Jan 4.

Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China

Under anoxic conditions, many bacteria, including strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in PV-4 and several other denitrifying species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and NO gases. Deletion of either of the NO-forming nitrite reductase genes or blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as -β (), , and were upregulated by CRP1, while transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions. Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of NO, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of NO emission from nitrate-rich and carbon source-poor waters and soils.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.01964-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783327PMC
January 2021

Links among extracellular enzymes, lignin degradation and cell growth establish the models to identify marine lignin-utilizing bacteria.

Environ Microbiol 2021 01 3;23(1):160-173. Epub 2020 Nov 3.

Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.

A major conundrum in the isolation of prokaryotes from open environments is stochasticity. It is especially difficult to study low abundance groups where very little biological information exists, although single-cell genomics and metagenomics have alleviated some of this bottleneck. Here, we report an approach to capture lignin-utilizing bacteria by linking a physical model to actual organisms. Extracellular enzymes, lignin degradation and cell growth are crucial phenotypes of lignin-utilizing bacteria, but their interrelationships remain poorly understood. In this study, the phenotypes of bacteria isolated from in situ lignocellulose enrichment samples in coastal waters were traced and statistically analysed. It suggested cell growth, dye-decolorizing peroxidase (DyP) and reactive oxygen species (ROS) were significantly correlated with lignin degradation, exhibiting a genus-specific property. The established models enabled us to efficiently capture lignin-utilizing bacteria and rapidly evaluate lignin degradation for Bacillus and Vibrio strains. Through the model, we identified several previously unrecognized marine bacterial lignin degraders. Moreover, it demonstrated that the isolated marine lignin-utilizing bacteria employ a DyP-based system and ROS for lignin depolymerization, providing insights into the mechanism of marine bacterial lignin degradation. Our findings should have implications beyond the capture of lignin-utilizing bacteria, in the isolation of other microorganisms with as-yet-unknown molecular biomarkers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.15289DOI Listing
January 2021

Root exudates drive soil-microbe-nutrient feedbacks in response to plant growth.

Plant Cell Environ 2021 Feb 22;44(2):613-628. Epub 2020 Nov 22.

Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China.

Although interactions between plants and microbes at the plant-soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow- and fast-growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient-depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate-treated soils, with similar responses observed for slow-growing and fast-growing plant exudate treatments. The fast-growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow-growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pce.13928DOI Listing
February 2021

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.

Nat Commun 2020 09 29;11(1):4897. Epub 2020 Sep 29.

College of Letters and Sciences, Faculty of Science and Mathematics, Arizona State University, Mesa, AZ, USA.

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-18706-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524716PMC
September 2020

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.

PLoS One 2020 28;15(9):e0232437. Epub 2020 Sep 28.

Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232437PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521895PMC
October 2020

A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming.

Nat Commun 2020 09 18;11(1):4717. Epub 2020 Sep 18.

Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.

Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-18560-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7501310PMC
September 2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.

ISME J 2020 11 15;14(11):2862-2876. Epub 2020 Sep 15.

Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-020-00753-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7784701PMC
November 2020

Microbial functional genes commonly respond to elevated carbon dioxide.

Environ Int 2020 11 29;144:106068. Epub 2020 Aug 29.

Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China. Electronic address:

Atmospheric CO concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO enrichment (FACE) experimental sites have shown significant impacts of elevated CO (eCO) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envint.2020.106068DOI Listing
November 2020

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments.

Microbiome 2020 08 31;8(1):126. Epub 2020 Aug 31.

State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China.

Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown.

Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat.

Conclusions: Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-020-00902-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460792PMC
August 2020

Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments.

Sci Total Environ 2021 Jan 4;750:141513. Epub 2020 Aug 4.

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China. Electronic address:

Excessive nitrate in water systems is prevailing and a global risk of human health. Polluted river sediments are dominated by anaerobes and often the hotspot of denitrification. So far, little is known about the ecological effects of nitrate pollution on microbial dynamics, especially those in sulfide-rich sediments. Here we simulated a nitrate surge and monitored the microbial responses, as well as the changes of important environmental parameters in a sulfide-rich river sediment for a month. Our analysis of sediment microbial communities showed that elevated nitrate led to (i) a functional convergence at denitrification and sulfide oxidation, (ii) a taxonomic convergence at Proteobacteria, and (iii) a significant loss of biodiversity, community stability and other functions. Two chemolithotrophic denitrifiers Thiobacillus and Luteimonas were enriched after nitrate amendment, although the original communities were dominated by methanogens and syntrophic bacteria. Also, serial dilutions of sediment microbial communities found that Thiobacillus thiophilus dominated 18/30 communities because of its capability of simultaneous nitrate reduction and sulfide oxidation. Additionally, our network analysis indicated that keystone taxa seemed more likely to be native auxotrophs (e.g., syntrophic bacteria, methanogens) rather than dominant denitrifiers, possibly because of the extensive interspecific cross-feeding they estabilished, while environment perturbations probably disrupted that cross-feeding and simplified microbial interactions. This study advances our understanding of microbial community responses to nitrate pollution and possible mechanism in the sulfide-rich river sediment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.141513DOI Listing
January 2021

Phytomanagement Reduces Metal Availability and Microbial Metal Resistance in a Metal Contaminated Soil.

Front Microbiol 2020 7;11:1899. Epub 2020 Aug 7.

Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Padua, Italy.

Short rotation coppice (SRC) with metal tolerant plants may attenuate the pollution of excessive elements with potential toxicity in soils, while preserving soil resources and functionality. Here, we investigated effects of 6 years phytomanagement with willow SRC on properties including heavy metal levels, toxicity tested by BioTox, microbial biomass, enzyme activities, and functional gene abundances measured by GeoChip of soils contaminated by As, Cd, Pb and Zn, as compared to the same soils under non-managed mixed grassland representing no intervention treatment (Unt). Though metal total concentrations did not differ by SRC and Unt, SRC soils had lower metal availability and toxicity, higher organic carbon, microbial biomass, phosphatase, urease and protease activities, as compared to Unt soils. Significantly reduced abundances of genes encoding resistances to various metals and antibiotics were observed in SRC, likely attributed to reduced metal selective pressure based on less heavy metal availability and soil toxicity. SRC also significantly reduced abundances of genes involved in nitrogen, phosphorus, and sulfur cycles, possibly due to the willow induced selection. Overall, while the SRC phytomanagement did not reduce the total heavy metal concentrations in soils, it decreased the heavy metal availability and soil toxicity, which in turn led to less metal selective pressure on microbial communities. The SRC phytomanagement also reduced the abundances of nutrient cycling genes from microbial communities, possibly due to intense plant nutrient uptake that depleted soil nitrogen and phosphorus availability, and thus site-specific practices should be considered to improve the soil nutrient supply for phytomanagement plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.01899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426507PMC
August 2020

Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature.

mBio 2020 08 18;11(4). Epub 2020 Aug 18.

Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA

Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes. Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00569-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7439460PMC
August 2020