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Appl Environ Microbiol 2022 May 24:e0046822. Epub 2022 May 24.

Department of Earth System Science, Stanford University, Stanford, California, USA.

Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Read More

Nat Commun 2022 May 23;13(1):2857. Epub 2022 May 23.

Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany.

Signal transduction via phosphorylated CheY towards the flagellum and the archaellum involves a conserved mechanism of CheY phosphorylation and subsequent conformational changes within CheY. This mechanism is conserved among bacteria and archaea, despite substantial differences in the composition and architecture of archaellum and flagellum, respectively. Phosphorylated CheY has higher affinity towards the bacterial C-ring and its binding leads to conformational changes in the flagellar motor and subsequent rotational switching of the flagellum. Read More

Comput Biol Chem 2022 Apr 30;98:107691. Epub 2022 Apr 30.

Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA. Electronic address:

Methanogenic archaea carry homologs of dissimilatory sulfite reductase (Dsr), called Dsr Like proteins (DsrLP). Dsr reduces sulfite to sulfide, a key step in an Earth's ancient metabolic process called dissimilatory sulfate reduction. The DsrLPs do not function as Dsr, and a computational approach is needed to develop hypotheses for guiding wet bench investigations on DsrLP's function. Read More

PLoS Genet 2022 May 23;18(5):e1010220. Epub 2022 May 23.

Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. Read More

Appl Environ Microbiol 2022 May 23:e0210921. Epub 2022 May 23.

Division of Geological and Planetary Sciences, California Institute of Technologygrid.20861.3d, Pasadena, California, USA.

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Read More

mSystems 2022 May 23:e0134821. Epub 2022 May 23.

Institute of Microbiology, Technische Universität Dresden, Dresden, Germany.

Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Read More

iScience 2022 May 29;25(5):104333. Epub 2022 Apr 29.

Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.

The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the and genes of AOA were found below the euphotic zone. Read More

Front Microbiol 2022 6;13:883738. Epub 2022 May 6.

Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain.

The gut microbiota is now recognised as a key target for improving aquaculture profit and sustainability, but we still lack insights into the activity of microbes in fish mucosal surfaces. In the present study, a metatranscriptomic approach was used to reveal the expression of gut microbial genes in the farmed gilthead sea bream. Archaeal and viral transcripts were a minority but, interestingly and contrary to rRNA amplicon-based studies, fungal transcripts were as abundant as bacterial ones, and increased in fish fed a plant-enriched diet. Read More

Environ Microbiome 2022 May 22;17(1):27. Epub 2022 May 22.

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e. Read More

Environ Pollut 2022 May 19:119477. Epub 2022 May 19.

CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, PR China; College of Life Sciences, Yantai University, Yantai, 264005, PR China. Electronic address:

This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Read More

Environ Sci Pollut Res Int 2022 May 20. Epub 2022 May 20.

Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.

Conversion of coastal mudflats into paddy soils is an effective measure to alleviate the pressures on land resources. However, few studies have evaluated the effects of nitrogen (N) fertilizers on bacterial communities in newly reclaimed mudflat paddy soils. We performed a field plot experiment with six N fertilizer rates (0, 210, 255, 300, 345, and 390 kg N ha) in a newly reclaimed mudflat paddy for 2 consecutive years and used Illumina sequencing and qPCR to investigate the effects of N fertilizers on bacterial communities and N-cycling genes. Read More

Brief Bioinform 2022 May 21. Epub 2022 May 21.

Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR.

Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Read More

Cell Host Microbe 2022 May 10. Epub 2022 May 10.

State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China. Electronic address:

Argonaute (Ago) proteins are widespread nucleic-acid-guided enzymes that recognize targets through complementary base pairing. Although, in eukaryotes, Agos are involved in RNA silencing, the functions of prokaryotic Agos (pAgos) remain largely unknown. In particular, a clade of truncated and catalytically inactive pAgos (short pAgos) lacks characterization. Read More

J Environ Manage 2022 May 17;316:115271. Epub 2022 May 17.

The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China. Electronic address:

Comammox bacteria have proved to be one dominant and significant ammonia-oxidizing microorganisms (AOMs) in municipal wastewater treatment plants (WWTPs), however, it still remains unknown about their abundance and diversity in industrial WWTPs. In this study, activated sludge samples from 8 municipal WWTPs and 6 industrial WWTPs treating refinery wastewater were taken and analyzed using qPCR and amoA gene sequencing. Intriguingly, quantitative real-time PCR (qPCR) results suggested that comammox bacteria had a higher numerical abundance compared with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in municipal WWTPs but did not in refinery WWTPs. Read More

J Hepatol 2022 Jun;76(6):1379-1391

Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA. Electronic address:

Humans harbour large quantities of microbes, including bacteria, fungi, viruses and archaea, in the gut. Patients with liver disease exhibit changes in the intestinal microbiota and gut barrier dysfunction. Preclinical models demonstrate the importance of the gut microbiota in the pathogenesis of various liver diseases. Read More

Methods Enzymol 2022 30;668:61-85. Epub 2021 Dec 30.

Department of Plant & Microbial Biology, University of California, Berkeley, CA, United States. Electronic address:

Cobamides are a family of enzyme cofactors that are required by organisms in all domains of life. Over a dozen cobamides exist in nature although only cobalamin (vitamin B), the cobamide required by humans, has been studied extensively. Cobamides are exclusively produced by a subset of prokaryotes. Read More

Methods Enzymol 2022 10;668:109-123. Epub 2022 Jan 10.

Department of Microbiology, University of Georgia, Athens, GA, United States. Electronic address:

Cobamides are essential for the performance of a variety of reactions such methyl transfers, carbon skeleton rearrangements, and eliminations in both prokaryotes and eukaryotes. However, cobamide biosynthesis is limited to a subset of bacteria and archaea. The biosynthesis pathway culminates with the activation and attachment of a lower ligand to the corrin ring; this branch of the pathway is known as nucleotide loop assembly (NLA) pathway. Read More

PLoS One 2022 19;17(5):e0268157. Epub 2022 May 19.

AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia.

Fermentation of pasture grasses and grains in the rumen of dairy cows and other ruminants produces methane as a by-product, wasting energy and contributing to the atmospheric load of greenhouse gasses. Many feeding trials in farmed ruminants have tested the impact of dietary components on feed efficiency, productivity and methane yield (MeY). Such diets remodel the rumen microbiome, altering bacterial, archaeal, fungal and protozoan populations, with an altered fermentation outcome. Read More

Nature 2022 May 18. Epub 2022 May 18.

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.

Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown. Read More

Biol Rev Camb Philos Soc 2022 May 18. Epub 2022 May 18.

School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA.

Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as 'biocrust', it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. Read More

Int J Syst Evol Microbiol 2022 May;72(5)

State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.

A novel methylotrophic methanogen sp. nov. was isolated from East China Sea sediment. Read More

Nat Commun 2022 May 16;13(1):2700. Epub 2022 May 16.

Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden.

Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Read More

Nat Commun 2022 May 16;13(1):2697. Epub 2022 May 16.

Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.

Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. Read More

Front Microbiol 2022 29;13:868383. Epub 2022 Apr 29.

Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India.

is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome-metabolite mining of . A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Read More

J Adv Res 2022 05 11;38:41-54. Epub 2021 Aug 11.

Institute of Geography, Fujian Normal University, Fuzhou 350007, China.

Introduction: Soil biota plays a crucial role in the terrestrial ecosystem. There is growing momentum to understand the community structure and diversity of total belowground soil biota across large ecological scales. Soil biota follow divergent trends with respect to soil physiochemical properties in different ecosystems; however, little is known about their response to stand development across multiple soil depths in Chinese fir plantations, which is the most important tree species across all over China, popular for its timber production. Read More

Front Chem 2022 27;10:871509. Epub 2022 Apr 27.

State Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Processing and Engineering, Chinese Academy of Sciences, Beijing, China.

The pandemic caused by SARS-CoV-2 is the most widely spread disease in the 21st century. Due to the continuous emergence of variants across the world, it is necessary to expand our understanding of host-virus interactions and explore new agents against SARS-CoV-2. In this study, it was found exopolysaccharides (EPSs) from halophilic archaeon ATCC33960 can bind to the spike protein of SARS-CoV-2 with the binding constant K of 2. Read More

Mol Biol Rep 2022 May 14. Epub 2022 May 14.

Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.

Background: The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system was initially identified in bacteria and archaea as a defense mechanism to confer immunity against phages. Later on, it was developed as a gene editing tool for both prokaryotic and eukaryotic cells including plant cells.

Methods And Results: CRISPR/Cas9 approach has wider applications in reverse genetics as well as in crop improvement. Read More

Mol Ecol 2022 May 13. Epub 2022 May 13.

School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS, USA.

The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Read More

Animals (Basel) 2022 Apr 20;12(9). Epub 2022 Apr 20.

Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA.

The ruminal microbiota of Angus cows and steers were characterized using 16s rRNA gene sequencing, and the expression of their metabolic pathways was predicted. Samples were collected on weaning day from the steers and the cows, and subsequently on three other occasions from the steers. Results showed that microbial richness, evenness, and diversity decreased ( < 0. Read More

Int J Environ Res Public Health 2022 05 8;19(9). Epub 2022 May 8.

Department of Civil and Environmental Engineering, Cleveland State University, FH 112, 2121 Euclid Ave, Cleveland, OH 44115, USA.

In wastewater treatment plants (WWTP), anaerobic digester (AD) units are commonly operated under mesophilic and thermophilic conditions. In some cases, during the dry season, maintaining a stable temperature in the digester requires additional power to operate a conditioning system. Without proper conditioning systems, methanogens are vulnerable to temperature shifts. Read More