A Sub-Antarctic Peat Moss Metagenome Indicates Microbiome Resilience to Stress and Biogeochemical Functions of Early Paleozoic Terrestrial Ecosystems

Graham, Linda E.; Graham, James M.; Knack, Jennifer J.; Trest, Marie T.; Piotrowski, Michael; Arancibia-Ávila, Patricia

doi:10.1086/693019

Cited by 18 publications

(14 citation statements)

References 67 publications

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“…At increasing depths, the Methylomonas signal was eventually below detection, consistent with qPCR and microarray data from the same study site (Esson et al, 2016). Other studies also found that pMMO genes affiliated with Methylocystis and other Alphaproteobacteria methanotrophs tended to be more abundant, possibly owing to the acidic pH or to copper limitation (Chen et al, 2008;Kolb and Horn, 2012;Lin et al, 2014;Graham et al, 2017). Corroborating decades of interest in peatland systems, gene-centric analyses have reaffirmed the importance of Alphaproteobacteria methanotrophs in many of these acidic environments as natural filters of methane release.…”

Section: Thawing Arctic Permafrostsupporting

confidence: 64%

Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity

Smith¹,

Wrighton²

2019

Current Issues in Molecular Biology

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Methanotrophic microorganisms utilize methane as an electron donor and a carbon source. To date, the capacity to oxidize methane is restricted to microorganisms from three bacterial and one archaeal phyla. Most of our knowledge of methanotrophic metabolism has been obtained using highly enriched or pure cultures grown in the laboratory. However, many methanotrophs currently evade cultivation, thus metagenomics provides a complementary approach for gaining insight into currently unisolated microorganisms. Here we synthesize the studies using metagenomics to glean information about methanotrophs. We complement this summary with an analysis of methanotroph marker genes from 235 publicly available metagenomic datasets. We analyse the phylogenetic and environmental distribution of methanotrophs sampled by metagenomics. We also highlight metabolic insights that methanotroph genomes assembled from metagenomes are illuminating. In summary, metagenomics has increased methanotrophic foliage within the tree of life, as well as provided new insights into methanotroph metabolism, which collectively can guide new cultivation efforts. Lastly, given the importance of methanotrophs for biotechnological applications and their capacity to filter greenhouse gases from a variety of ecosystems, metagenomics will continue to be an important component in the arsenal of tools needed for understanding methanotroph diversity and metabolism in both engineered and natural systems.

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Section: Thawing Arctic Permafrostsupporting

confidence: 64%

Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity

Smith¹,

Wrighton²

2019

Current Issues in Molecular Biology

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“…As was the case for other bryophytes and streptophyte algae studied similarly 14 , 15 , the T. lepidozioides microbiome included microbial species known to promote plant growth. Burkholderia phytofirmans , detected by 279 bp of 23S rRNA gene sequence that was 100% similar to database references, is a known plant growth promoter, as is Variovorax paradoxa S110, indicated by 302 bp of 23S rRNA gene sequence that was 99.8% similar to references.…”

Section: Resultsmentioning

confidence: 85%

“…Metagenomic evidence for genus Rhizobium in the T. lepidozioides microbiome–indicated by both ribosomal and nifH marker genes–was shared with aquatic Coleochaetales streptophyte algae and rock-dwelling Conocephalum conicum (liverwort) previously studied using similar preparation methods 14 . Bradyrhizobium was observed to be a relatively-abundant associate shared with Sphagnum fimbriatum 15 , representing Sphagnales, which are close moss relatives of Takakiales 1 . These commonalities suggest that N-fixing bacterial associations likely aided plant N-acquisition long before the evolution of root nodules in angiosperms.…”

Section: Resultsmentioning

confidence: 99%

“…Contigs assembled from metagenomic data were used for taxonomic assessments to improve identification confidence, because matches occurred over longer sequence regions than was the case for short reads more commonly employed 11 . Results were compared to metagenomic and symbiosis-related structural features we had previously described for other bryophytes and streptophyte algae that had been sampled, processed, and analyzed similarly, to facilitate evolutionary contrasts 12 – 15 .…”

Section: Introductionmentioning

confidence: 99%

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Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes

Satjarak

Golinski

Trest

et al. 2022

Sci Rep

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Origin of earliest land plants from ancestral algae dramatically accelerated the evolution of Earth’s terrestrial ecosystems, in which microbial symbioses have played key roles. Recent molecular diversification analyses identify the rare, geographically-limited moss Takakia as Earth’s most archaic modern land plant. Despite occupying a phylogenetic position pivotal for understanding earliest plants, Takakia microbial associations are poorly known. Here, we describe symbiosis-related structural features and contig-based metagenomic data that illuminate the evolutionary transition from streptophyte algae to early embryophytes. We observed that T. lepidozioides shares with streptophyte algae secretion of microbe-harboring mucilage and bacterial taxa such as Rhizobium and genes indicating nitrogen fixation. We find that Takakia root-analogs produce lateral mucilage organs that are more complex than generally understood, having structural analogies to angiosperm lateral roots adapted for N-fixation symbioses, including presence of intracellular microbes. We also find structural and metagenomic evidence for mycorrhiza-like species of glomalean fungi (including Rhizophagus irregularis) not previously known for mosses, as well as ascomycete fungi (e.g. Rhizoscyphus ericae) that associate with other early-diverging plants. Because Takakia is the oldest known modern plant genus, this study of plants of a remote locale not strongly influenced by human activities may indicate microbiome features of early land plants.

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“…Novosphingobium is reported associated with the gut of Cryptocephalus spp. (Chrysomelidae; Montagna et al, 2014), Anoplophora glabripennis (Cerambycidae;Geib et al, 2009), oral secretions of Curculionidae (Cardoza et al, 2009), herbivorous Cicadellidae (Rogers, 2016), gall midges (Ojha et al, 2017) and also mosses (Bragina et al, 2012;Graham et al, 2017). Ralstonia is a plant-associated genus abundant in the microbiota of Cicadellidae (Rogers & Backus, 2014), Cryptocephalus spp.…”

Section: Ecology and Function Of Potential Symbiontsmentioning

confidence: 99%

High-diversity microbiomes in the guts of bryophagous beetles (Coleoptera: Byrrhidae)

Pyszko¹,

Šigut²,

Kostovčík³

et al. 2019

Eur. J. Entomol.

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http://www.eje.cz al., 2002) and kairomones (Leroy et al., 2011), or mating attractiveness (Sharon et al., 2010). Their benefi cial role in diet processing through degradation of complex food components (Warnecke et al., 2007) and toxins (Kikuchi et al., 2012), nitrogen fi xation (Nikoh et al., 2011), ammonia recycling (Hongoh et al., 2008), and nutrient supplementation via the synthesis of vitamins (Akman et al., 2002) and essential amino acids (Douglas, 1998) is also crucial. Whereas the microbiota of xylophagous and herbivorous insects has been extensively studied, the microbiome of bryophagous (moss-feeding) insects has remained poorly characterized, except for an obligate endosymbiotic taxon in the bacteriomes of moss bugs (Hemiptera: Peloridiidae; Kuechler et al., 2013). At present, nothing is known about microbial assemblages in the guts or abdomens of

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A Sub-Antarctic Peat Moss Metagenome Indicates Microbiome Resilience to Stress and Biogeochemical Functions of Early Paleozoic Terrestrial Ecosystems

Cited by 18 publications

References 67 publications

Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity

Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity

Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes

High-diversity microbiomes in the guts of bryophagous beetles (Coleoptera: Byrrhidae)

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