Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents

Anderson, R.; Sogin, Mitchell L.; Baross, John A.

doi:10.1093/femsec/fiu016

Cited by 70 publications

(62 citation statements)

References 44 publications

(25 reference statements)

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“…This study agrees with other surveys showing rare microbial taxa have greater geographical structuring than abundant taxa (e.g. Nemergut et al, 2011;Oono et al, 2014;Anderson et al, 2015) as well as theoretical expectations that abundance and distribution are correlated (Sloan et al, 2006). Our spatially stratified sampling design should impede inherent biases of many amplicon sequencing methods (i.e.…”

Section: Distance Decay In Fungal Endophytes 2799supporting

confidence: 91%

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Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Oono

Rasmussen

Lefèvre

2017

Environmental Microbiology

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Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities. We report multiple distance-decay patterns consistent with effects of dispersal limitation, largely driven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads per sample on average. Distance-decay rates and community structure also depended on specific classes of fungi and were predominantly influenced by rare members of Dothideomycetes. Communities separated by urban areas also revealed stronger effects of distance on community similarity, confirming that host density and diversity plays an important role in symbiont biogeography, which may ultimately lead to a mosaic of functional diversity as well as rare species diversity across landscapes.

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Section: Distance Decay In Fungal Endophytes 2799supporting

confidence: 91%

“…This study agrees with other surveys showing rare microbial taxa have greater geographical structuring than abundant taxa (e.g. Nemergut et al ., ; Oono et al ., ; Anderson et al ., ) as well as theoretical expectations that abundance and distribution are correlated (Sloan et al ., ).…”

Section: Discussionmentioning

confidence: 67%

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Oono

Rasmussen

Lefèvre

2017

Environmental Microbiology

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“…These viruses were novel with a majority of the viral protein products having no characterized homologs. The viral genomes were not integrated within their host genomes in the metagenome assembly, suggesting that most of the viruses were lytic rather than lysogenic, in contrast to viruses found in high temperature environments (Anderson et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

Crits-Christoph

Gelsinger

et al. 2016

Environmental Microbiology

111

133

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Halite endoliths in the Atacama Desert represent one of the most extreme ecosystems on Earth. Cultivation-independent methods were used to examine the functional adaptations of the microbial consortia inhabiting halite nodules. The community was dominated by haloarchaea and functional analysis attributed most of the autotrophic CO2 fixation to one unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a 'salt-in' strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to 'salt-in' strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses and predominance of a 'salt-in' strategy to balance the high osmotic pressure of the environment.

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“…Classic sulfur-oxidizing bacteria have been detected as the dominant families, suggesting a strong sulfur-metabolizing potential in all tested chimney samples (Table 3). Many members within Epsilon - and Gammaproteobacteria are known to be chemoautotrophs utilizing inorganic sulfur as election donor to gain energy (Nakagawa et al, 2005; Yamamoto and Takai, 2011; Anderson et al, 2015). The deep-sea chemoautotrophic Gammaproteobacteria , possess two different sulfur-oxidization pathways including the reverse sulfate reduction and the Sox multienzyme system without SoxCD, and strictly require co-existence of reduced sulfur compounds and O 2 (Yamamoto and Takai, 2011).…”

Section: Discussionmentioning

confidence: 99%

Microbial Community Structure of Deep-sea Hydrothermal Vents on the Ultraslow Spreading Southwest Indian Ridge

et al. 2017

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Southwest Indian Ridge (SWIR) is a typical oceanic ultraslow spreading ridge with intensive hydrothermal activities. The microbial communities in hydrothermal fields including primary producers to support the entire ecosystem by utilizing geochemical energy generated from rock-seawater interactions. Here we have examined the microbial community structures on four hydrothermal vents from SWIR, representing distinct characteristics in terms of temperature, pH and metal compositions, by using Illumina sequencing of the 16S small subunit ribosomal RNA (rRNA) genes, to correlate bacterial and archaeal populations with the nature of the vents influenced by ultraslow spreading features. Epsilon-, Gamma-, Alpha-, and Deltaproteobacteria and members of the phylum Bacteroidetes and Planctomycetes, as well as Thaumarchaeota, Woesearchaeota, and Euryarchaeota were dominant in all the samples. Both bacterial and archaeal community structures showed distinguished patterns compared to those in the fast-spreading East Pacific Ridge or the slow-spreading Mid-Atlantic Ridge as previously reported. Furthermore, within SWIR, the microbial communities are highly correlated with the local temperatures. For example, the sulfur-oxidizing bacteria were dominant within bacteria from low-temperature vents, but were not represented as the dominating group recovered from high temperature (over 300°C) venting chimneys in SWIR. Meanwhile, Thaumarchaeota, the ammonium oxidizing archaea, only showed high relative abundance of amplicons in the vents with high-temperature in SWIR. These findings provide insights on the microbial community in ultraslow spreading hydrothermal fields, and therefore assist us in the understanding of geochemical cycling therein.

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Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents

Cited by 70 publications

References 44 publications

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

Microbial Community Structure of Deep-sea Hydrothermal Vents on the Ultraslow Spreading Southwest Indian Ridge

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