Publications by authors named "Nianzhi Jiao"

212 Publications

Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale.

Environ Int 2021 Apr 23;154:106558. Epub 2021 Apr 23.

State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China. Electronic address:

Dissolved organic matter (DOM) changes in quantity and quality over time and space, especially in highly dynamic coastal estuaries. Bacterioplankton usually display seasonal and spatial variations in abundance and composition in the coastal regions, and influence the DOM pool via assimilation, transformation and release of organic molecules. The change in DOM can also affect the composition of bacterial community. However, little is known on the correspondence between DOM molecules and bacterial composition, particularly through a systematic field survey. In this study, the spatiotemporal signatures of microbial communities and DOM composition in the subtropical coastal estuary of Xiamen are investigated over one and half years. The co-occurrence analysis between bacteria and DOM suggested microorganisms likely transformed the DOM from a relatively high (>400 Da) to a low (<400 Da) molecular weight, corresponding to an apparent increase in overall aromaticity. This might be the reason why microbial transformation renders "dark" organic matter visible in mass spectrometry due to more efficient ionization of microbial metabolites, as well as photodegradation processes. K- and r-strategists exhibited different correlations with two-size categories of DOM molecules owing to their different lifestyles and responses to environmental nutrient conditions. A comparison of the environmental variables and DOM composition with the microbial communities showed that the environmental/DOM variations played a more important role in shaping the microbial communities than vice versa. This study sheds light on the interactions between microbial populations and DOM molecules at the spatiotemporal scale, improving our understanding of microbial roles in marine biogeochemical cycles.
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http://dx.doi.org/10.1016/j.envint.2021.106558DOI Listing
April 2021

Water mass shapes the distribution patterns of planktonic ciliates (Alveolata, Ciliophora) in the subtropical Pearl River Estuary.

Mar Pollut Bull 2021 Apr 14;167:112341. Epub 2021 Apr 14.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China. Electronic address:

Ciliates comprise essential components of microzooplankton in diverse marine environments. However, the extent to which environmental variables shape the distribution of planktonic ciliates in complex estuarine systems remains unclear. Here, 52 samples were collected from the Pearl River Estuary, China to reveal the influence of environmental variables on planktonic ciliate communities. Distinct community compositions of ciliates were found in three identified water masses: Pearl River diluted water mass, South China Sea surface water mass, and South China Sea bottom water mass. Significant differences in abundance, biomass, cell size, and oral diameter structure of ciliates were also detected among the three water masses. The partial Mantel test showed that water mass (as represented by water temperature and salinity) surpassed other environmental variables to be the primary factor driving the dynamics of the ciliate community. This study revealed the controlling mechanisms of planktonic ciliate communities in a subtropical, hydrographically complex estuarine ecosystem.
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http://dx.doi.org/10.1016/j.marpolbul.2021.112341DOI Listing
April 2021

Correcting a major error in assessing organic carbon pollution in natural waters.

Sci Adv 2021 Apr 14;7(16). Epub 2021 Apr 14.

State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China.

Microbial degradation of dissolved organic carbon (DOC) in aquatic environments can cause oxygen depletion, water acidification, and CO emissions. These problems are caused by labile DOC (LDOC) and not refractory DOC (RDOC) that resists degradation and is thus a carbon sink. For nearly a century, chemical oxygen demand (COD) has been widely used for assessment of organic pollution in aquatic systems. Here, we show through a multicountry survey and experimental studies that COD is not an appropriate proxy of microbial degradability of organic matter because it oxidizes both LDOC and RDOC, and the latter contributes up to 90% of DOC in high-latitude forested areas. Hence, COD measurements do not provide appropriate scientific information on organic pollution in natural waters and can mislead environmental policies. We propose the replacement of the COD method with an optode-based biological oxygen demand method to accurately and efficiently assess organic pollution in natural aquatic environments.
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http://dx.doi.org/10.1126/sciadv.abc7318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8046372PMC
April 2021

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms.

Microbiome 2021 03 24;9(1):71. Epub 2021 Mar 24.

State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.

Background: Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles.

Results: We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina.

Conclusions: The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.
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http://dx.doi.org/10.1186/s40168-021-01022-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7992965PMC
March 2021

Complete Genome Sequence of Chesapeake Bay Winter sp. Strain CBW1107, a Member of Subalpine Cluster II.

Microbiol Resour Announc 2021 Feb 18;10(7). Epub 2021 Feb 18.

Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA

Here, we report the complete genome sequence of psychrotolerant sp. strain CBW1107, which was isolated from the Chesapeake Bay in winter. CBW1107 is a member of picocyanobacterial subalpine cluster II and exhibits greater cold tolerance than do most coastal and marine strains.
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http://dx.doi.org/10.1128/MRA.01399-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7892667PMC
February 2021

Biogeographical Distribution and Community Assembly of Active Protistan Assemblages Along an Estuary to a Basin Transect of the Northern South China Sea.

Microorganisms 2021 Feb 10;9(2). Epub 2021 Feb 10.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.

Marine protists are essential for globally critical biological processes, including the biogeochemical cycles of matter and energy. However, compared with their prokaryotic counterpart, it remains largely unclear how environmental factors determine the diversity and distribution of the active protistan communities on the regional scale. In the present study, the biodiversity, community composition, and potential drivers of the total, abundant, and rare protistan groups were studied using high throughput sequencing on the V9 hyper-variable regions of the small subunit ribosomal RNA (SSU rRNA) along an estuary to basin transect in the northern South China Sea. Overall, Bacillariophyta and Cercozoa were abundant in the surface water; heterotrophic protists including Spirotrichea and marine stramenopiles 3 (MAST-3) were more abundant in the subsurface waters near the heavily urbanized Pearl River estuary; Chlorophyta and Pelagophyceae were abundant at the deep chlorophyll maximum depth, while Hacrobia, Radiolaria, and Excavata were the abundant groups in the deep water. Salinity, followed by water depth, temperature, and other biological factors, were the primary factors controlling the distinct vertical and horizontal distribution of the total and abundant protists. Rare taxa were driven by water depth, followed by temperature, salinity, and the concentrations of PO. The active protistan communities were mainly driven by dispersal limitation, followed by drift and other ecological processes.
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http://dx.doi.org/10.3390/microorganisms9020351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916720PMC
February 2021

Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter.

Environ Microbiol 2021 Feb 8. Epub 2021 Feb 8.

State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.

Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.
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http://dx.doi.org/10.1111/1462-2920.15426DOI Listing
February 2021

Complete Genome Sequences of Chesapeake Bay Synechococcus Strains CBW1002 and CBW1006 Isolated in Winter.

Genome Biol Evol 2021 Feb;13(2)

The Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA.

Synechococcus are picocyanobacteria with a cosmopolitan distribution. They are capable of surviving in a wide variety of environmental conditions. Synechococcus have been isolated from the Chesapeake Bay during winter months, and they show an impressive tolerance to cold temperatures. Cold-adapted Synechococcus are unique and diverse, as they have complex phylogenetic lineages closely related to subalpine cluster II, Bornholm Sea cluster, CB7 cluster, and some novel lineages which are independent from summer estuarine strains in subcluster 5.2. CBW1002 and CBW1006 are the first complete genomes to represent Bornholm Sea cluster Synechococcus strains. They have some of the largest genomes among the Synechococcus (3.8 Mb) and share many unique and cryptic homologs which could give insight into their ability to tolerate such cold and dynamic conditions in the Chesapeake Bay estuary.
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http://dx.doi.org/10.1093/gbe/evab009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7881327PMC
February 2021

The genomic content and context of auxiliary metabolic genes in roseophages.

Environ Microbiol 2021 Jan 28. Epub 2021 Jan 28.

State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China.

Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG), most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.
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http://dx.doi.org/10.1111/1462-2920.15412DOI Listing
January 2021

Elevated Contribution of Low Nucleic Acid Prokaryotes and Viral Lysis to the Prokaryotic Community Along the Nutrient Gradient From an Estuary to Open Ocean Transect.

Front Microbiol 2020 15;11:612053. Epub 2020 Dec 15.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.

Prokaryotes represent the largest living biomass reservoir in aquatic environments and play a crucial role in the global ocean. However, the factors that shape the abundance and potential growth rate of the ecologically distinct prokaryotic subgroups [i.e., high nucleic acid (HNA) and low nucleic acid (LNA) cells] along varying trophic conditions in the ocean remain poorly understood. This study conducted a series of modified dilution experiments to investigate how the abundance and potential growth rate of HNA and LNA prokaryotes and their regulating factors (i.e., protozoan grazing and viral lysis) change along a cross-shore nutrient gradient in the northern South China Sea. The results showed that the abundance of both HNA and LNA cells was significantly positively correlated with the abundance of heterotrophic nanoflagellates and viruses, whereas only HNA abundance exhibited a significant positive correlation with nutrient level. With a decreasing nutrient concentration, the potential growth rate of the HNA subgroup declined significantly, while that of the LNA subgroup was significantly enhanced, leading to an elevated relative potential growth rate of the LNA to HNA subgroup under decreasing nutrient levels. Furthermore, our data revealed different regulatory roles of protozoan grazing and viral lysis on the HNA and LNA subgroups, with HNA suffering higher mortality pressure from grazing than from lysis in contrast to LNA, which experienced equivalent pressures. As the nutrient levels declined, the relative contribution of lysis to the mortality of the HNA subgroup increased significantly, in contrast to the insignificant change in that of the LNA subgroup. Our results indicated the elevated role of LNA cells in the prokaryotic community and the enhanced viral lysis pressure on the total prokaryotes under oligotrophic conditions. This implies a weakened efficiency of carbon cycling within the microbial loop and enhanced viral lysis to shunt more carbon and energy flow in the future ocean, in which oligotrophication will be strengthened due to global warming.
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http://dx.doi.org/10.3389/fmicb.2020.612053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793805PMC
December 2020

Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China.

Front Microbiol 2020 23;11:592489. Epub 2020 Dec 23.

State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.

Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.
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http://dx.doi.org/10.3389/fmicb.2020.592489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7785585PMC
December 2020

Bacteria in the lakes of the Tibetan Plateau and polar regions.

Sci Total Environ 2021 Feb 7;754:142248. Epub 2020 Sep 7.

Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

The Tibetan Plateau, also termed 'the Third Pole' harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142248DOI Listing
February 2021

Top-down controls on nutrient cycling and population dynamics in a model estuarine photoautotroph-heterotroph co-culture system.

Mol Ecol 2021 01 6;30(2):592-607. Epub 2020 Dec 6.

State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.

Viral lysis and protistan grazing are thought to be the major processes leading to microbial mortality in aquatic environments and thus regulate community diversity and biogeochemical cycling characteristics. Here, we studied nutrient cycling and bacterial responses to cyanophage-mediated photoautotroph lysis and ciliate predation in a model Synechococcus-heterotroph co-culture system. Both viral lysis and Euplotes grazing facilitated the transformation of organic carbon from biomass to dissolved organic matter with convention efficiencies of 20%-26%. The accumulation of ammonium after the addition of phages and ciliates suggested the importance of recycled NH occurred in the interactions between Synechococcus growth and heterotrophic bacterial metabolism of photosynthate. The slower efficiency of P mineralization compared to N (primarily ammonium) indicated that P-containing organic matter was primarily integrated into bacterial biomass rather than being remineralized into inorganic phosphate under C-rich conditions. In the cyanophage addition treatment, both Fluviicola and Alteromonas exhibited rapid positive responses to Synechococcus lysing, while Marivita exhibited an apparent negative response. Further, the addition of Euplotes altered the incubation system from a Synechococcus-driven phycosphere to a ciliate-remodelled zoosphere that primarily constituted grazing-resistant bacteria and Euplotes symbionts. Top-down controls increased co-culture system diversity and resulted in a preference for free-living lifestyles of dominant populations, which was accompanied by the transfer of matter and energy. Our results indicate top-down control was particularly important for organic matter redistribution and inorganic nutrient regeneration between photoautotrophs and heterotrophs, and altered bacterial lifestyles. This study consequently sheds light on marine biogeochemical cycling and the interaction networks within these dynamic ecosystems.
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http://dx.doi.org/10.1111/mec.15750DOI Listing
January 2021

Viral Lysis Alters the Optical Properties and Biological Availability of Dissolved Organic Matter Derived from Picocyanobacteria.

Appl Environ Microbiol 2021 01 15;87(3). Epub 2021 Jan 15.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China

Phytoplankton contribute almost half of the world's total primary production. The exudates and viral lysates of phytoplankton are two important forms of dissolved organic matter (DOM) in aquatic environments and fuel heterotrophic prokaryotic metabolism. However, the effect of viral infection on the composition and biological availability of phytoplankton-released DOM is poorly understood. Here, we investigated the optical characteristics and microbial utilization of the exudates and viral lysates of the ecologically important unicellular picophytoplankton Our results showed that DOM produced by viral lysis (Pro-vDOM) with phages of three different morphotypes (myovirus P-HM2, siphovirus P-HS2, and podovirus P-SSP7) had higher humic-like fluorescence intensities, lower absorption coefficients, and higher spectral slopes than DOM exuded by (Pro-exudate). The results indicate that viral infection altered the composition of -derived DOM and might contribute to the pool of oceanic humic-like DOM. Incubation with Pro-vDOM resulted in a greater dissolved organic carbon (DOC) degradation rate and lower absorption spectral slope and heterotrophic bacterial growth rate than incubation with Pro-exudate, suggesting that Pro-vDOM was more bioavailable than Pro-exudate. In addition, the stimulated microbial community succession trajectories were significantly different between the Pro-exudate and Pro-vDOM treatments, indicating that viral lysates play an important role in shaping the heterotrophic bacterial community. Our study demonstrated that viral lysis altered the chemical composition and biological availability of DOM derived from , which is the numerically dominant phytoplankton in the oligotrophic ocean. The unicellular picocyanobacterium is the numerically dominant phytoplankton in the oligotrophic ocean, contributing to the vast majority of marine primary production. releases a significant fraction of fixed organic matter into the surrounding environment and supports a vital portion of heterotrophic bacterial activity. Viral lysis is an important biomass loss process of However, little is known about whether and how viral lysis affects -released dissolved organic matter (DOM). Our paper shows that viral infection alters the optical properties (such as the absorption coefficients, spectral slopes, and fluorescence intensities) of released DOM and might contribute to a humic-like DOM pool and carbon sequestration in the ocean. Meanwhile, viral lysis also releases various intracellular labile DOM, including amino acids, protein-like DOM, and lower-molecular-weight DOM, increases the bioavailability of DOM, and shapes the successive trajectory of the heterotrophic bacterial community. Our study highlights the importance of viruses in impacting the DOM quality in the ocean.
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http://dx.doi.org/10.1128/AEM.02271-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848921PMC
January 2021

T4-like myovirus community shaped by dispersal and deterministic processes in the South China Sea.

Environ Microbiol 2021 02 3;23(2):1038-1052. Epub 2020 Nov 3.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China.

As the most abundant and genetically diverse biological entities, viruses significantly influence ecological, biogeographical and evolutionary processes in the ocean. However, the biogeography of marine viruses and the drivers shaping viral community are unclear. Here, the biogeographic patterns of T4-like viruses and the relative impacts of deterministic (environmental selection) and dispersal (spatial distance) processes were investigated in the northern South China Sea. The dominant viral operational taxonomic units were affiliated with previously defined Marine, Estuary, Lake and Paddy Groups. A clear viral biogeographic pattern was observed along the environmental gradient from the estuary to open sea. Marine Groups I and IV had a wide geographical distribution, whereas Marine Groups II, III and V were abundant in lower-salinity continental or eutrophic environments. A significant distance-decay pattern was noted for the T4-like viral community, especially for those infecting cyanobacteria. Both deterministic and dispersal processes influenced viral community assembly, although environmental selection (e.g. temperature, salinity, bacterial abundance and community, etc.) had a greater impact than spatial distance. Network analysis confirmed the strong association between viral and bacterial community composition, and suggested a diverse ecological relationship (e.g. lysis, co-infection or mutualistic) between and within viruses and their potential bacterial hosts.
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http://dx.doi.org/10.1111/1462-2920.15290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7984403PMC
February 2021

Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench and Bacteria Based on Single-Cell Genomics Analyses.

Front Microbiol 2020 24;11:1739. Epub 2020 Jul 24.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.

Heterotrophic bacteria such as those from the group and genus dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to and , recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal and SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal and lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in and bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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http://dx.doi.org/10.3389/fmicb.2020.01739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393951PMC
July 2020

DOC dynamics and bacterial community succession during long-term degradation of Ulva prolifera and their implications for the legacy effect of green tides on refractory DOC pool in seawater.

Water Res 2020 Oct 4;185:116268. Epub 2020 Aug 4.

Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address:

Under climate warming and coastal eutrophication, outbreaks of green tides have increased in recent decades; e.g., the world's largest green tide caused by Ulva prolifera has occurred in the Yellow Sea for 13 consecutive years. The massive assemblage of macroalgae absorbs large amounts of atmospheric CO and converts it into biomass. After the green tide, millions of tons of the macroalgal biomass sink to the seabed to be degraded eventually; this inevitably has a significant impact on the coastal organic carbon pool and microbial community. However, this impact is poorly understood. Here, the degradation of Ulva prolifera over 520 days revealed that relatively sufficient degradation of the macroalgae occurred at ca. 7 months. The rapid release of dissolved organic carbon (DOC) mainly occurred in the first week, which not only increased the size and diversity of the DOC pool in a short time but also promoted the rapid growth of bacteria and led to hypoxia and acidification of the seawater. After that, the labile portion of DOC was gradually used up by bacteria within one month, while the degradation of semi-labile or semi-refractory DOC occurred in half a year. The remaining DOC existed in the form of refractory DOC (RDOC), resisting bacterial consumption and remaining stable for 10 months. During the long-term degradation process, bacterial community structure and metabolic function showed obvious successional characteristics, driving the gradual transformation of DOC from labile to refractory through the microbial carbon pump mechanism. After the long-term degradation, the remaining RDOC accounted for approximately 1.6% of the macroalgal carbon biomass. As RDOC can maintain long-term stability, we propose that the frequent outbreaks of green tides not only affect microbial processes but also may have an important cumulative effect on the coastal RDOC pool.
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http://dx.doi.org/10.1016/j.watres.2020.116268DOI Listing
October 2020

Contrasting Community Composition of Active Microbial Eukaryotes in Melt Ponds and Sea Water of the Arctic Ocean Revealed by High Throughput Sequencing.

Front Microbiol 2020 3;11:1170. Epub 2020 Jun 3.

Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea.

Melt ponds (MPs), form as the result of thawing of snow and sea ice in the summer, have lower albedo than the sea ice and are thus partly responsible for the polar amplification of global warming. Knowing the community composition of MP organisms is key to understanding their roles in the biogeochemical cycles of nutrients and elements. However, the community composition of MP microbial eukaryotes has rarely been studied. In the present study, we assessed the microbial eukaryote biodiversity, community composition, and assembly processes in MPs and surface sea water (SW) using high throughput sequencing of 18S rRNA of size-fractionated samples. Alpha diversity estimates were lower in the MPs than SW across all size fractions. The community composition of MPs was significantly different from that of SW. The MP communities were dominated by members from Chrysophyceae, the ciliate classes Litostomatea and Spirotrichea, and the cercozoan groups Filosa-Thecofilosea. One open MP community was similar to SW communities, which was probably due to the advanced stage of development of the MP enabling the exchange of species between it and adjacent SW. High portions of shared species between MPs and SW may indicate the vigorous exchange of species between these two major types of environments in the Arctic Ocean. SW microbial eukaryote communities are mainly controlled by dispersal limitation whereas those of MP are mainly controlled by ecological drift.
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http://dx.doi.org/10.3389/fmicb.2020.01170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291953PMC
June 2020

Coupling Between Carbon and Nitrogen Metabolic Processes Mediated by Coastal Microbes in -Derived Organic Matter Addition Incubations.

Front Microbiol 2020 25;11:1041. Epub 2020 May 25.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.

Phytoplankton are major contributors to labile organic matter in the upper ocean. Diverse heterotrophic bacteria successively metabolize these labile compounds and drive elemental biogeochemical cycling. We investigated the bioavailability of -derived organic matter (SOM) by estuarine and coastal microbes during 180-day dark incubations. Variations in organic carbon, inorganic nutrients, fluorescent dissolved organic matter (FDOM), and total/active microbial communities were monitored. The entire incubations could be partitioned into three phases (labeled I, II, and III) based on the total organic carbon (TOC) consumption rates of 6.38-7.01, 0.53-0.64, and 0.10-0.13 μmol C L day, respectively. This corresponded with accumulation processes of NH, NO, and NO, respectively. One tryptophan-like (C1) and three humic-like (C2, C3, and C4) FDOM components were identified. The intensity variation of C1 followed bacterial growth activities, and C2, C3, and C4 displayed labile, semi-labile, and refractory DOM characteristics, respectively. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Actinobacteria dominated the quickly consumed process of SOM (phase I) coupled with a substantial amount of NH generation. Thaumarchaeota became an abundant population with the highest activities in phase II, especially in the free-living size-fraction, and these organisms could perform chemoautotroph processes through the ammonia oxidation. Microbial populations frequently found in the dark ocean, even the deep sea, became abundant during phase III, in which Nitrospinae/Nitrospirae obtained energy through nitrite oxidation. Our results shed light on the transformation of different biological availability of organic carbon by coastal microorganisms which coupled with the regeneration of different form of inorganic nitrogen.
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http://dx.doi.org/10.3389/fmicb.2020.01041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261836PMC
May 2020

Spatial distribution patterns of planktonic ciliate communities in the East China Sea: Potential indicators of water masses.

Mar Pollut Bull 2020 Jul 17;156:111253. Epub 2020 May 17.

State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China. Electronic address:

The spatial distribution of planktonic ciliates over the coastal and continental shelf of the East China Sea were investigated using quantative protargol staining. Aloricate oligotrichs and choreotrichs were dominant in terms of species number, abundance and biomass. Ciliate densities varied between 3 and 2688 cells L with higher values occurring in the coastal water and the mixing water than in the Yellow Sea coastal water and the Taiwan warm water. Ciliate biomass exhibited a similar pattern as abundance. A canonical analysis of principal coordinates demonstrated that the spatial patterns of ciliate community structure could be clearly discriminated in different water masses. Diversity parameters showed strong relationships with spatial changes in ciliate communities and might serve as predictors of water mass in future studies. Our findings provide evidence for using ciliate communtiy composition, supplemented with dominant species and diversity parameters, as potential indicators of water masses in complex marine environments.
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http://dx.doi.org/10.1016/j.marpolbul.2020.111253DOI Listing
July 2020

Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes.

Sci Total Environ 2020 Sep 11;733:139216. Epub 2020 May 11.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China. Electronic address:

Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.
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http://dx.doi.org/10.1016/j.scitotenv.2020.139216DOI Listing
September 2020

Viral control of biomass and diversity of bacterioplankton in the deep sea.

Commun Biol 2020 May 22;3(1):256. Epub 2020 May 22.

State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), 361102, Xiamen, Fujian, China.

Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean. We observed a negative effect of viruses on prokaryotic abundance, indicating the top-down control of bacterioplankton by virioplankton in the deep-sea. The decreased bacterial diversity and a different bacterial community structure with diluted viruses indicate that viruses are sustaining a diverse microbial community in deep-sea environments. Network analysis showed that relieving viral pressure decreased the complexity and clustering coefficients but increased the proportion of positive correlations for the potentially active bacterial community, which suggests that viruses impact deep-sea bacterioplankton interactions. Our study provides experimental evidences of the crucial role of viruses in microbial ecology and biogeochemistry in deep-sea ecosystems.
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http://dx.doi.org/10.1038/s42003-020-0974-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244761PMC
May 2020

Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion.

Commun Biol 2020 03 5;3(1):98. Epub 2020 Mar 5.

State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.

Ferulic acid is a ubiquitous phenolic compound in lignocellulose, which is recognized for its role in the microbial carbon catabolism and industrial value. However, its recalcitrance and toxicity poses a challenge for ferulic acid-to-bioproducts bioconversion. Here, we develop a genome editing strategy for Pseudomonas putida KT2440 using an integrated CRISPR/Cas9n-λ-Red system with pyrF as a selection marker, which maintains cell viability and genetic stability, increases mutation efficiency, and simplifies genetic manipulation. Via this method, four functional modules, comprised of nine genes involved in ferulic acid catabolism and polyhydroxyalkanoate biosynthesis, were integrated into the genome, generating the KTc9n20 strain. After metabolic engineering and optimization of C/N ratio, polyhydroxyalkanoate production was increased to ~270 mg/L, coupled with ~20 mM ferulic acid consumption. This study not only establishes a simple and efficient genome editing strategy, but also offers an encouraging example of how to apply this method to improve microbial aromatic compound bioconversion.
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http://dx.doi.org/10.1038/s42003-020-0824-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058019PMC
March 2020

sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur.

mBio 2020 02 25;11(1). Epub 2020 Feb 25.

Institute of Marine Science and Technology, Shandong University, Qingdao, China

Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that sp. strain PCC7002 (PCC7002), harboring an gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S, present as persulfide and polysulfide in the cell. The Δ mutant contained less cellular S and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria. Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δ mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.
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http://dx.doi.org/10.1128/mBio.03420-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7042703PMC
February 2020

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Culture.

mBio 2020 02 18;11(1). Epub 2020 Feb 18.

State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China

Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including , , , , and The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to growth phases. Six high-quality genomes, including and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, , displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, and , and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the -heterotroph coculture system and the interactions shaping the system. The high complexity of ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of environments.
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http://dx.doi.org/10.1128/mBio.03261-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029141PMC
February 2020

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean.

Proc Natl Acad Sci U S A 2020 03 18;117(9):4823-4830. Epub 2020 Feb 18.

Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, A-1090 Vienna, Austria.

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 10 to ∼2 × 10 mol of C per year globally through the flux of ∼1 × 10 to ∼2 × 10 mol of N per year of the two steps of oxidation throughout the dark ocean.
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http://dx.doi.org/10.1073/pnas.1912367117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060736PMC
March 2020

Characteristics of two myoviruses induced from the coastal photoheterotrophic bacterium Porphyrobacter sp. YT40.

FEMS Microbiol Lett 2019 12;366(23)

State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.

In this study, we characterized two induced myoviruses from one marine photoheterotrophic bacterium Porphyrobacter sp. YT40 belonging to the Sphingomonadales family in Alphaproteobacteria. The genome sequence of prophage A is ∼36.9 kb with an average GC content of 67.1%, and its core or functional genes are homologous to Mu or Mu-like phages. Furthermore, induced viral particles from prophage A show a knob-like neck structure, which is only found in bacteriophage Mu. The genome size of prophage B is ∼36.8 kb with an average GC content of 65.3%. Prophage B contains a conserved gene cluster Q-P-O-N-M-L, which is unique in P2 phages. Induced viral particles from prophage B display an icosahedral head with a diameter of ∼55 nm and a 130 ± 5 nm long contractile tail. To our knowledge, this is the first report that characterizes the induced P2-like phage in marine Alphaproteobacteria. Phylogeny analyses suggest that these two types of prophages are commonly found in sequenced bacteria of the Sphingomonadales family. This study sheds light on the ongoing interaction between marine bacteria and phages, and improves our understanding of bacterial genomic plasticity and evolution.
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http://dx.doi.org/10.1093/femsle/fnaa009DOI Listing
December 2019

sp. nov., a marine bacterium isolated from surface sea water in the South China Sea.

Int J Syst Evol Microbiol 2020 Feb;70(2):958-963

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China.

A Gram-stain-negative and facultatively anaerobic bacterial strain, designated GUO, was isolated from surface water collected from the South China Sea. Cells were non-flagellate, yellow, non-spore-forming and rod-shaped. The 16S rRNA gene sequence comparisons with species in the genus showed that strain GUO shares the highest similarity of 97.5 % with and . Average nucleotide identity and digital DNA-DNA hybridization values between strain GUO and its related type strains were 77.1-78.4% and 20.8-26.2 % respectively. Growth of strain GUO occurred at 15-50°C (optimum, 20-25°C), pH 5-7.5 (pH 6) and in media containing 0-7 % NaCl (optimum, 0-1 %). Cells contained methanol-soluble yellow-coloured pigments but flexirubin-type pigments were absent. The major fatty acids (>5 %) were iso-C 3-OH, iso-C, anteiso-C, C, summed feature 3, iso-C G and iso-C 3-OH. The dominant polar lipids comprised phosphatidylethanolamine and some unidentified polar lipids. The main respiratory quinone was menaquinone-6. The DNA G+C content of strain GUO was 40.1 %. Based on the presented data, we consider strain GUO to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is GUO (=KCTC 62629=MCCC 1K03559).
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http://dx.doi.org/10.1099/ijsem.0.003855DOI Listing
February 2020

sp. nov., isolated from marine sediment.

Int J Syst Evol Microbiol 2020 Feb;70(2):868-873

Institute of Marine Science and Technology, Shandong University, Qingdao 266273, PR China.

A novel, Gram-stain-negative, motile, flagellated, aerobic, rod-shaped (0.5-0.7 µm wide and 1.0-1.2 µm long) and faint-yellow strain, designated ALS 84, was isolated from marine sediment sampled at Ailian bay, Rongcheng, PR China. Growth occurred in the presence of 1-3 % (w/v) NaCl (optimum, 2 % NaCl), at pH 4.0-8.0 (pH 6.0-7.0) and at 8-30 °C (28 °C). The genome size was 4.37 Mbp. The G+C content of the genomic DNA was 33.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences suggested that strain ALS 84 belongs to the genus within the family , and is most closely related to (95.6 % similarity). The major fatty acids (>10 %) were iso-C 3-OH (22.9 %), iso-C (14.0 %) and C (10.9 %). The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone-6 (MK-6) was identified as the respiratory quinone. On the basis of the phenotypic, phylogenetic and chemotaxonomic data obtained in the study, strain ALS 84 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the novel species is strain ALS 84 (=KCTC 62398=MCCC 1K03480).
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http://dx.doi.org/10.1099/ijsem.0.003839DOI Listing
February 2020

A newly isolated roseophage represents a distinct member of Siphoviridae family.

Virol J 2019 11 6;16(1):128. Epub 2019 Nov 6.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.

Background: Members of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts' population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade.

Methods: vB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis.

Results: The double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the 'cohesive ends' DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean.

Conclusions: Information about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.
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http://dx.doi.org/10.1186/s12985-019-1241-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836515PMC
November 2019