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Soil microbiomes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.

Lawrence P Wackett,

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):753-754]

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Anaerobic oxidation of methane mediated by microbial extracellular respiration.

Xueqin Zhang, Zhiguo Yuan, Shihu Hu,

Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Cyanobacterial community composition and their functional shifts associated with biocrust succession in the Gurbantunggut Desert.

Shubin Lan, Andrew David Thomas, Julie Bethany Rakes, Ferran Garcia-Pichel, Li Wu, Chunxiang Hu,

Cyanobacteria, as key biocrust components, provide a variety of ecosystem functions in drylands. In this study, to identify whether a cyanobacterial community shift is involved in biocrust succession and whether this is linked to altered ecological functions, we investigated cyanobacterial composition, total carbon and nitrogen contents of biocrusts in the ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria.

Hong-Yan Bai, Ai-Yue Zhang, Yan Mei, Man Xu, Xiao-Lin Lu, Chuan-Chao Dai, Yong Jia,

Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Unique bacterial communities and potential function along the vertical gradient in the deepest marine blue hole.

Yuxuan Zhang, Huitao Xu, Liping Wang, Ruizhi Liu, Liang Fu, Kuixuan Lin,

The Sansha Yongle Blue Hole is the deepest blue hole in the world discovered so far, while its great potential and values have not been fully exploited regarding microbial communities. A large-scale sampling was performed at different depths (0-270 m) inside the blue hole. Based on high-throughput sequencing, the diversity and ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Chances and limitations when uncovering essential and non-essential genes of Bacillus subtilis phages with CRISPR-Cas9.

Katharina Kohm, Syamantak Basu, Muhammad M Nawaz, Robert Hertel,

Virulent bacterial viruses, also known as phages or bacteriophages, are considered as a potential option to fight antibiotic-resistant bacteria. However, their biology is still poorly understood, and only a fraction of phage genes is assigned with a function. To enable the first classification, we explored new options to test phage ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Genomic attributes differ between Vibrio parahaemolyticus environmental and clinical isolates including pathotypes.

Divya Meparambu Prabhakaran, Hardip R Patel, Sivakumar Sivakumar Krishnankutty Chandrika, Sabu Thomas,

Vibrio parahaemolyticus is a marine bacterium and causes opportunistic gastroenteritis in humans. Clinical strains of V. parahaemolyticus contain haemolysin and type III secretion systems (T3SS) that define their pathotype. A growing number of strains isolated recently from the environment have acquired these virulence genes constituting a pool of potential pathogens. ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Soil pH and moisture govern the assembly processes of abundant and rare bacterial communities in a dryland montane forest.

Jianming Wang, Mingxu Li, Jingwen Li,

The assembly mechanisms and ecological drivers of abundant and rare bacterial subcommunities in dryland montane forest ecosystems remain unclear. Here, we compared the biogeographic patterns of rare and abundant bacterial subcommunities and examined the ecological drivers governing their assembly processes in a dryland montane forest of China. Our results showed ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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The ubiquitous soil verrucomicrobial clade 'Candidatus Udaeobacter' shows preferences for acidic pH.

Inka M Willms, Simon H Bolz, Jingyue Yuan, Lisa Krafft, Dominik Schneider, Ingo Schöning, Marion Schrumpf, Heiko Nacke,

Members of the verrucomicrobial clade 'Candidatus Udaeobacter' rank among the most dominant bacterial phylotypes in soil. Nevertheless, despite this global prevalence, in-depth analyses with respect to pH preferences of 'Ca. Udaeobacter' representatives are still lacking. Here, we utilized a recently designed primer pair, specifically targeting 'Ca. Udaeobacter', to investigate links ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Biogeographic structure of fungal communities in seagrass Halophilia ovalis across the Malay Peninsula.

Z B Randolph Quek, Geoffrey Zahn, Nicole Li Ying Lee, Jillian Lean Sim Ooi, Jen Nie Lee, Danwei Huang, Benjamin J Wainwright,

Distributed across both the tropical Atlantic and Pacific oceans, the seagrass Halophilia ovalis stabilizes coastal sediment, thereby preventing shoreline erosion and is also an important food source for megaherbivores such as dugongs. However, seagrass meadows globally are under severe duress due to both climate change and anthropogenic activities. We characterized ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Bacillus thuringiensis RZ2MS9, a tropical plant growth-promoting rhizobacterium, colonizes maize endophytically and alters the plant's production of volatile organic compounds during co-inoculation with Azospirillum brasilense Ab-V5.

Jaqueline Raquel de Almeida, Maria Letícia Bonatelli, Bruna Durante Batista, Natalia Sousa Teixeira-Silva, Mateus Mondin, Rafaela Cristina Dos Santos, José Maurício Simões Bento, Carolina Alessandra de Almeida Hayashibara, João Lúcio Azevedo, Maria Carolina Quecine,

The beneficial features of Bacillus thuringiensis (Bt) are not limited to its role as an insecticide; it is also able to promote plant growth interacting with plants and other plant growth-promoting rhizobacterium (PGPR). The PGPR Bt strain RZ2MS9 is a multi-trait maize growth promoter. We obtained a stable mutant of ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Herbivory shapes the rhizosphere bacterial microbiota in potato plants.

Antonino Malacrinò, Mingyuan Wang, Sandra Caul, Alison J Karley, Alison E Bennett,

Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Rapid formation of mature microbialites in Lake Alchichica, Mexico.

Miguel Iniesto, David Moreira, Karim Benzerara, Elodie Muller, Paola Bertolino, Rosaluz Tavera, Purificación López-García,

Microbialites are emblematic sedimentary rocks formed by phylogenetically and metabolically complex microbial communities thriving under specific physicochemical conditions. Most microbialites are photosynthesis-based ecosystems frequently formed by carbonates, thereby capturing inorganic carbon in the form of both, organic matter and mineral precipitates. However, little is known about the amount of sequestered ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):600-605]

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Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation.

Siavash Atashgahi, Margreet J Oosterkamp, Peng Peng, Jeroen Frank, Beate Kraft, Bastian Hornung, David Schleheck, Sebastian Lücker, Mike S M Jetten, Alfons J M Stams, Hauke Smidt,

Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms.

Tal Zvi-Kedem, Eli Shemesh, Dan Tchernov, Maxim Rubin-Blum,

The symbioses between the vestimentiferan tubeworms and their chemosynthetic partners (Gammaproteobacteria, Chromatiales and Sedimenticolaceae) hallmark the success of these organisms in hydrothermal vent and hydrocarbon seep deep-sea habitats. The fidelity of these associations varies, as both the hosts and the symbionts can be loose in partner choice. Some tubeworms may ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):744-752]

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Genotypes and phenotypes of methicillin-resistant staphylococci isolated from shrimp aquaculture farms.

Vineeth Rajan, Gopalan Krishnan Sivaraman, Ardhra Vijayan, Ravikrishnan Elangovan, Alison Prendiville, Till T Bachmann,

The population of methicillin-resistant (MR) staphylococci in aquatic environment is rarely investigated. Here, we characterized a collection of MR staphylococci recovered from shrimp aquaculture farms (n = 37) in Kerala, India. A total of 261 samples yielded 47 MR isolates (16 S. aureus, 13 S. haemolyticus, 11 S. epidermidis, 3 S. saprophytics and 2 each of ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Microbes and climate change: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.

Lawrence P Wackett,

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(4):555-556]

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The potential of Pseudomonas for bioremediation of oxyanions.

Sofía Vieto, Diego Rojas-Gätjens, José I Jiménez, Max Chavarría,

Non-metal, metal and metalloid oxyanions occur naturally in minerals and rocks of the Earth's crust and are mostly found in low concentrations or confined in specific regions of the planet. However, anthropogenic activities including urban development, mining, agriculture, industrial activities and new technologies have increased the release of oxyanions to ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei.

Katarzyna Garbacz, Roman Kotłowski, Ewa Kwapisz,

The aim of our study was to assess the sequencing of unique nucH gene fragment based on performed bioinformatics analysis as a novel diagnostic method for the identification of difficult to identify staphylococcal human pathogenic strains. Initially, PCR-RFLP-rrn analysis specific to the spacers between 16SrDNA and 23SrDNA followed by HhaI ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):735-743]

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Disentangling soil microbiome functions by perturbation.

Adam Ossowicki, Jos M Raaijmakers, Paolina Garbeva,

Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):582-590]

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The two-component system RstAB regulates production of a polysaccharide capsule with a role in virulence in the marine pathogen Photobacterium damselae subsp. damselae.

Xosé M Matanza, Laura López-Suárez, Ana do Vale, Carlos R Osorio,

The marine bacterium Photobacterium damselae subsp. damselae (Pdd) causes disease in marine animals and in humans. Previous studies demonstrated that mutation of the two-component system RstAB strongly impacts virulence of this pathogen, but the RstAB regulon has not been thoroughly elucidated. We here compared the transcriptomes of Pdd RM-71 and ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Rapid detection of temperate bacteriophage using a simple motility assay.

Yunxue Guo, Jianzhong Lin, Xiaoxue Wang,

Phage contamination is a common complication for the fermentation and pharmaceutical industries. The risk of bacteriophage contamination in laboratory processes increases with multiple rounds of genetic manipulation such as deletion and complementation. The contamination of temperate phages does not lead to immediate host cell lysis but could become a serious ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):728-734]

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Metagenomic and metatranscriptomic analysis reveals enrichment for xenobiotic-degrading bacterial specialists and xenobiotic-degrading genes in a Canadian Prairie two-cell biobed system.

Jennifer N Russell, Benjamin J Perry, Jordyn Bergsveinson, Claire N Freeman, Claudia Sheedy, Denise Nilsson, Larry Braul, Christopher K Yost,

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, the microbiomes in these environments remain largely understudied both taxonomically and functionally. This study used ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(5):720-727]

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Bacteriophage therapeutics to confront multidrug-resistant Acinetobacter baumannii - a global health menace.

Sandhya Rai, Amod Kumar,

We have already entered the post-antibiotic era as the outbreaks of numerous multidrug-resistant strains in the community as well as hospital-acquired infections are ringing alarm bells in the health sector. Acinetobacter baumannii is one such pathogen that has been considered a worldwide threat as it acquires multidrug resistance. It is ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, :]

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Multiple plant hormone catabolism activities: an adaptation to a plant-associated lifestyle by Achromobacter spp.

Francisco X Nascimento, Bernard R Glick, Márcio J Rossi,

Elaborating the plant hormone catabolic activities of bacteria is important for developing a detailed understanding of plant-microbe interactions. In this work, the plant hormone catabolic and plant growth promotion activities of Achromobacter xylosoxidans SOLR10 and A. insolitus AB2 are described. The genome sequences of these strains were obtained and analysed ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2021, 13(4):533-539]

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