Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity DOI Creative Commons
Ashley Shade, Stuart E. Jones, J. Gregory Caporaso

et al.

mBio, Journal Year: 2014, Volume and Issue: 5(4)

Published: July 16, 2014

ABSTRACT Microbial communities typically contain many rare taxa that make up the majority of observed membership, yet contribution this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing 3,237 samples from 42 time series nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant brewery wastewater treatment), we introduce a new method detect occasionally become very abundant (conditionally [CRT]) then quantify their contributions temporal shifts in structure. We discovered CRT made 1.5 28% represented broad diversity bacterial archaeal lineages, explained large amounts dissimilarity (i.e., 97% Bray-Curtis dissimilarity). Most were detected at multiple points, though also identified “one-hit wonder” only one point. case study temperate lake, gained additional insights into ecology by comparing routine disturbance events. Our results reveal contribute greater amount than apparent low proportional abundances. This observation was true across wide range ecosystems, indicating these are essential for understanding changes over time. IMPORTANCE processes foundations ecosystems. The ecological roles microorganisms largely unknown, but it thought they stability acting as reservoir can rapidly respond environmental changes. investigated occurrence more prominent (“conditionally rare”). quantified conditionally variety not present all examples, contributed disproportionately when most abundant. result indicates an important general role within communities.

Language: Английский

Microbial interactions: from networks to models DOI
Karoline Faust, Jeroen Raes

Nature Reviews Microbiology, Journal Year: 2012, Volume and Issue: 10(8), P. 538 - 550

Published: July 16, 2012

Language: Английский

Citations

3266
Decoupling function and taxonomy in the global ocean microbiome DOI

Stilianos Louca,

Laura Wegener Parfrey, Michael Doebeli

et al.

Science, Journal Year: 2016, Volume and Issue: 353(6305), P. 1272 - 1277

Published: Sept. 15, 2016

Microbial metabolism powers biogeochemical cycling in Earth’s ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes this variation remain largely unknown. We analyzed and functional community profiles to determine factors that shape marine bacterial archaeal across global ocean. By classifying >30,000 microorganisms into metabolic groups, we were able disentangle from variation. find environmental conditions strongly influence distribution groups by shaping niches, only weakly within individual groups. Hence, structure constitute complementary roughly independent “axes variation” shaped markedly different processes.

Language: Английский

Citations

2633
Structure and function of the global ocean microbiome DOI
Shinichi Sunagawa, Luís Pedro Coelho, Samuel Chaffron

et al.

Science, Journal Year: 2015, Volume and Issue: 348(6237)

Published: May 22, 2015

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture functional diversity, microbial community structure, and their ecological determinants remains grand challenge. We analyzed 7.2 terabases metagenomic data from 243 Tara Oceans samples 68 locations in epipelagic mesopelagic waters across the globe to generate an ocean reference gene catalog with >40 million nonredundant, mostly novel sequences viruses, prokaryotes, picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification composition driven by temperature rather than other environmental factors or geography. identify core functionality reveal that >73% its abundance is shared human gut microbiome despite physicochemical differences between these two ecosystems.

Language: Английский

Citations

2609
Molecular ecological network analyses DOI Creative Commons
Ye Deng,

Yi‐Huei Jiang,

Yunfeng Yang

et al.

BMC Bioinformatics, Journal Year: 2012, Volume and Issue: 13(1)

Published: May 30, 2012

Understanding the interaction among different species within a community and their responses to environmental changes is central goal in ecology. However, defining network structure microbial very challenging due extremely high diversity as-yet uncultivated status. Although recent advance of metagenomic technologies, such as throughout sequencing functional gene arrays, provide revolutionary tools for analyzing structure, it still difficult examine interactions based on high-throughput metagenomics data. Here, we describe novel mathematical bioinformatics framework construct ecological association networks named molecular (MENs) through Random Matrix Theory (RMT)-based methods. Compared other construction methods, this approach remarkable that automatically defined robust noise, thus providing excellent solutions several common issues associated with We applied determine communities subjected long-term experimental warming pyrosequencing data 16 S rRNA genes. showed constructed MENs under both unwarming conditions exhibited topological features scale free, small world modularity, which were consistent previously described networks. Eigengene analysis indicated eigengenes represented module profiles relatively well. In consistency many studies, major traits including temperature soil pH found be important determining examined. To facilitate its application by scientific community, all these methods statistical have been integrated into comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), open-accessible now ( http://ieg2.ou.edu/MENA ). The RMT-based provides powerful elucidate changes, are fundamentally research ecology microbiology.

Language: Английский

Citations

2547
Keystone taxa as drivers of microbiome structure and functioning DOI
Samiran Banerjee, Klaus Schlaeppi, Marcel G. A. van der Heijden

et al.

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(9), P. 567 - 576

Published: May 22, 2018

Language: Английский

Citations

2146
Patterns and Processes of Microbial Community Assembly DOI Open Access

Diana R. Nemergut,

Steven K. Schmidt, Tadashi Fukami

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2013, Volume and Issue: 77(3), P. 342 - 356

Published: Sept. 1, 2013

Recent research has expanded our understanding of microbial community assembly. However, the field ecology is inaccessible to many ecologists because inconsistent and often confusing terminology as well unnecessarily polarizing debates. Thus, we review recent literature on assembly, using framework Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort synthesize unify these contributions. We begin by discussing patterns biogeography then describe four basic processes (diversification, dispersal, selection, drift) that contribute also discuss different combinations where when they may be most important for shaping communities. The spatial temporal scales assembly are discussed relation processes. Throughout this paper, highlight differences between microbes macroorganisms generate hypotheses describing how end implications ecosystem function biodiversity.

Language: Английский

Citations

1626
Fundamentals of Microbial Community Resistance and Resilience DOI Creative Commons
Ashley Shade, Hannes Peter, Steven Allison

et al.

Frontiers in Microbiology, Journal Year: 2012, Volume and Issue: 3

Published: Jan. 1, 2012

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure predict. Understanding drivers stability, including resistance (insensitivity disturbance) resilience (the rate recovery after is important for predicting response disturbance. Here, we provide an overview concepts stability that relevant communities. First, highlight insights from ecology useful defining measuring stability. To determine whether general disturbance responses exist communities, next examine representative studies literature investigated press (long-term) pulse (short-term) disturbances a variety habitats. Then discuss biological features individual microorganisms, populations, may govern overall We conclude with thoughts about unique systems perspectives - informed by meta-omics data

Language: Английский

Citations

1400
Species-level functional profiling of metagenomes and metatranscriptomes DOI
Eric A. Franzosa, Lauren J. McIver, Ali Rahnavard

et al.

Nature Methods, Journal Year: 2018, Volume and Issue: 15(11), P. 962 - 968

Published: Oct. 23, 2018

Language: Английский

Citations

1366
Climate warming enhances microbial network complexity and stability DOI
Mengting Yuan, Xue Guo, Linwei Wu

et al.

Nature Climate Change, Journal Year: 2021, Volume and Issue: 11(4), P. 343 - 348

Published: Feb. 22, 2021

Language: Английский

Citations

1350
The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota) DOI Open Access
Maarja Öpik,

Alo Vanatoa,

Elise Vanatoa

et al.

New Phytologist, Journal Year: 2010, Volume and Issue: 188(1), P. 223 - 241

Published: June 16, 2010

• Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate description distribution richness patterns in this group fungi. Small subunit (SSU) rRNA gene sequences metadata were collated from all suitable taxonomic ecological publications. These have been made accessible an open-access (http://maarjam.botany.ut.ee). Two hundred eighty-two SSU virtual taxa (VT) described based on comprehensive phylogenetic analysis sequences. Two-thirds VT showed limited ranges, occurring single current or historic continents climatic zones. Those with taxonomically wide range host plants also tended geographical distribution, vice versa. No relationships detected between latitude, elevation vascular plant richness. molecular diversity suggest ranges most positive relationship width taxon's its range. Inconsistencies traditional taxonomy Glomeromycota, shortage major ecosystems, are highlighted.

Language: Английский

Citations

1015