Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Applied and Environmental Microbiology, Год журнала: 2009, Номер 75(23), С. 7537 - 7541

Опубликована: Окт. 3, 2009

ABSTRACT mothur aims to be a comprehensive software package that allows users use single piece of analyze community sequence data. It builds upon previous tools provide flexible and powerful for analyzing sequencing As case study, we used trim, screen, align sequences; calculate distances; assign sequences operational taxonomic units; describe the α β diversity eight marine samples previously characterized by pyrosequencing 16S rRNA gene fragments. This analysis more than 222,000 was completed in less 2 h with laptop computer.

Язык: Английский

---

Multivariate analyses in microbial ecology

FEMS Microbiology Ecology, Год журнала: 2007, Номер 62(2), С. 142 - 160

Опубликована: Сен. 24, 2007

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable better identification diversity patterns, but also shed more light on associated conditions, spatial locations, seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, represent vast potential techniques that are still underexploited. Here, well-established exploratory hypothesis-driven approaches reviewed, so as foster their addition microbial ecologist toolbox. Because tools aim at reducing data set complexity, identifying major patterns putative causal factors, they certainly find many applications in ecology.

Язык: Английский

---

Distinct soil microbial diversity under long-term organic and conventional farming

The ISME Journal, Год журнала: 2014, Номер 9(5), С. 1177 - 1194

Опубликована: Окт. 28, 2014

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production ecosystem health. Despite integral role soil microbiome production, we still have a limited understanding complex response microbial diversity organic conventional farming. Here report on structural more than two decades different management long-term field experiment using high-throughput pyrosequencing approach bacterial fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion shifted structure microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed quality fertilizers, as differences became smaller an integrated fertilization scheme were examined. The impact plant protection regime, characterized by moderate targeted application pesticides, subordinate importance. Systems not receiving manure harboured dispersed functionally versatile community presumably oligotrophic organisms adapted nutrient-limited environments. fertilizer specific guilds known be involved degradation compounds such compost. throughput resolution sequencing permitted detect shifts level individual taxa that harbours novel potential for managing environment means promoting beneficial suppressing detrimental organisms.

Язык: Английский

---

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Soil Biology and Biochemistry, Год журнала: 2011, Номер 43(7), С. 1450 - 1455

Опубликована: Апрель 15, 2011

Язык: Английский

---

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Янв. 16, 2018

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known which extent how specifically soil microbiomes can be manipulated through different cropping practices. Here, we investigated wheat root microbial communities in system experiment consisting of conventional organic managements, both with tillage intensities. While richness was marginally affected, found pronounced effects on community composition, were specific for the respective microbiomes. Soil bacterial primarily structured by tillage, whereas fungal responded mainly management type additional tillage. In roots, also driving factor bacteria but not fungi, generally determined changes intensity. To quantify an "effect size" microbiota manipulation, that about 10% variation explained tested Cropping sensitive taxonomically diverse, they guilds taxa These included frequent members or co-occurring many other community, suggesting practices may allow manipulation influential members. Understanding abundance patterns basis towards developing strategies smart farming. For future targeted management—e.g., foster certain practices—a next step will identify functional traits microbes.

Язык: Английский

---

Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

Journal of Experimental Botany, Год журнала: 2009, Номер 60(6), С. 1729 - 1742

Опубликована: Апрель 1, 2009

Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant–microbe interactions rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number naturally occurring ecotype accessions exist, lacks mycorrhizal associations and hence an ideal model studies. Eight were found exert marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) ribosomal intergenic spacer analysis (RISA). Community differences composition relative abundance both significant (P <0.001). The eight distinct reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates these variants analysed high performance liquid chromatography (HPLC) try establish whether unique assemblages among could attributed plant-regulated chemical changes rhizosphere. Natural variation root exudation patterns was clearly exhibited, suggesting that influencing bacterial assemblages. Other such system architecture probably involved. Finally, investigate further, phylogenetic diversity rhizobacteria accession Cvi-0 described.

Язык: Английский

---

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

Annual Review of Microbiology, Год журнала: 2008, Номер 62(1), С. 375 - 401

Опубликована: Июнь 10, 2008

Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space time. Although these are the major drivers biosphere processes, relatively little is known about their structure function, predictive modeling limited a dearth comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions central terms have been used in various fashions ecology, provide framework focusing on different types interactions within communities, review status interface between evolutionary study, highlight important similarities differences macro- ecology. We current approaches to study ecology progress toward modeling.

Язык: Английский

---

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

Applied and Environmental Microbiology, Год журнала: 2010, Номер 76(20), С. 6751 - 6759

Опубликована: Авг. 21, 2010

The diversity of bacteria in soil is enormous, and bacterial communities can vary greatly structure. Here, we employed a pyrosequencing-based analysis the V2-V3 16S rRNA gene region to characterize overall horizon-specific (A B horizons) community compositions nine grassland soils, which covered three different land use types. entire data set comprised 752,838 sequences, 600,544 could be classified below domain level. average number sequences per horizon was 41,824. dominant taxonomic groups present all samples horizons were Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, Bacteroidetes. Despite these overarching taxa, abundance, diversity, composition specific. In almost cases, estimated (H') higher A than corresponding horizons. addition, H' positively correlated with organic carbon content, total nitrogen C-to-N ratio, decreased depth. It appeared that lower intensity results diversity. majority affiliated Bacteroidetes, Cyanobacteria, Fibrobacteres, Spirochaetes, Verrucomicrobia, Gammaproteobacteria derived from horizons, whereas related Gemmatimonadetes, Nitrospira, TM7, WS3 originated distribution some phylogenetic subgroups properties such as or microbial biomass.

Язык: Английский

---

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

The ISME Journal, Год журнала: 2008, Номер 2(7), С. 689 - 695

Опубликована: Май 8, 2008

Язык: Английский

---

Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem

Soil Biology and Biochemistry, Год журнала: 2013, Номер 65, С. 86 - 95

Опубликована: Май 31, 2013

Язык: Английский

---