Microbiota and Host Nutrition across Plant and Animal Kingdoms

Cell Host & Microbe, Год журнала: 2015, Номер 17(5), С. 603 - 616

Опубликована: Май 1, 2015

Язык: Английский

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Geobacter

Advances in microbial physiology/Advances in Microbial Physiology, Год журнала: 2011, Номер unknown, С. 1 - 100

Опубликована: Янв. 1, 2011

Язык: Английский

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Revisiting life strategy concepts in environmental microbial ecology

FEMS Microbiology Ecology, Год журнала: 2017, Номер unknown, С. fix006 - fix006

Опубликована: Янв. 22, 2017

Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies determine at least to some extent prevalence distribution in the environment. Unlike animals plants, there is an unprecedented diversity intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based functional traits as has been done animal plant ecology challenging. Nevertheless, representative pure cultures, microbial distinguishing different had proposed, focus of previous reviews. In environment, however, vast majority naturally occurring have yet be isolated, restricting association broad phylogenetic groups and/or physiological characteristics. Here, we reviewed literature how strategy concepts (i.e. copio- oligotrophic strategists, competitor-stress tolerator-ruderals framework) applied complex communities. Because scarcity direct empirical evidence elucidating communities, rely heavily observational studies determining response (a)biotic cues (e.g. resource availability) infer strategies. Although our parallels were drawn from fungal community. Our search showed inconsistency community proposed copiotrophic- oligotrophic-associated (phyla level) changing environmental conditions. This suggests that tracking finer taxonomic resolution family level lower) may more effective capture changes edaphic factors exert a stronger effect response. We discuss limitations provide recommendations future research applying studies.

Язык: Английский

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Microbial Ecology of Methanogens and Methanotrophs

Advances in agronomy, Год журнала: 2007, Номер unknown, С. 1 - 63

Опубликована: Янв. 1, 2007

Язык: Английский

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The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance

Current Opinion in Biotechnology, Год журнала: 2006, Номер 17(3), С. 241 - 249

Опубликована: Май 16, 2006

Язык: Английский

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Ammonia‐oxidizing archaea: important players in paddy rhizosphere soil?

Environmental Microbiology, Год журнала: 2008, Номер 10(8), С. 1978 - 1987

Опубликована: Апрель 22, 2008

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase alpha-subunit (amoA) gene. Ammonia-oxidizing predominated among prokaryotes soil, AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. more abundant rhizosphere than bulk soil. Rice cultivation led greater abundance AOA AOB copies differences composition. These results show that is dominant this study, we assume influenced by exudation rice root (e.g. oxygen, carbon dioxide) AOB.

Язык: Английский

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Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

Applied Microbiology and Biotechnology, Год журнала: 2008, Номер 80(3), С. 365 - 380

Опубликована: Июль 21, 2008

Язык: Английский

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Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system

Applied Soil Ecology, Год журнала: 2015, Номер 99, С. 1 - 12

Опубликована: Ноя. 28, 2015

Язык: Английский

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Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils

Applied and Environmental Microbiology, Год журнала: 2017, Номер 83(9)

Опубликована: Март 4, 2017

ABSTRACT The possibility that Methanothrix (formerly Methanosaeta ) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated rice paddy soils. Genes with high sequence similarity to the gene for PilA pilin monomer of electrically conductive pili (e-pili) sulfurreducens accounted over half sequences metagenomic libraries 42% mRNA transcripts RNA sequencing (RNA-seq) libraries. This abundance e-pilin genes is significant because e-pili can serve as conduits DIET. Most were affiliated species, but most closely related putative from genera such Desulfobacterium , Deferribacter Geoalkalibacter Desulfobacula also detected. Approximately 17% all metatranscriptomic bacterial clustered finding spp. actively transcribing growth-related indicated they metabolically active coding among highly transcribed genes. In addition, homologs encoding OmcS, a c -type cytochrome associated G. required DIET, expressed soils enzymes involved reduction carbon dioxide methane. DIET only donor known support CO 2 . Thus, these results are consistent model which providing electrons methane production through electrical connections e-pili. IMPORTANCE some important microbial contributors global production, surprisingly little about their physiology ecology. source it demonstrates contribution makes may extend beyond conversion acetate Furthermore, defined coculture studies have suggested when receive energy grow faster than sole source. growth metabolism be more robust generally considered. suggest reason repeatedly found microorganisms syntrophically cooperation spp., possibly other methanogens,

Язык: Английский

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Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments

Environmental Microbiology, Год журнала: 2014, Номер 17(5), С. 1533 - 1547

Опубликована: Июль 25, 2014

Summary Syntrophic interaction occurs during anaerobic fermentation of organic substances forming methane as the final product. H 2 and formate are known to serve electron carriers in this process. Recently, it has been shown that direct interspecies transfer ( DIET ) for syntrophic CH 4 production from ethanol acetate. Here, we constructed paddy soil enrichments determine involvement butyrate oxidation production. The results showed was significantly accelerated presence nano Fe 3 O all continuous transfers. This acceleration increased with increase concentration but dismissed when coated silica insulated mineral electrical conduction. Nano particles were found closely attached cell surfaces different morphology, thus bridging connections. Molecular approaches, including DNA ‐based stable isotope probing, revealed bacterial S yntrophomonadaceae G eobacteraceae , archaeal M ethanosarcinaceae ethanocellales ethanobacteriales involved Among them, growth strictly relied on its conductivity particular. Other organisms, except present regardless amendment. Collectively, our study demonstrated ‐facilitated occurred butyrate, eobacter species played key role process enrichments.

Язык: Английский

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