New Microbial Biodiversity in Marine Sediments

Abstract

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling. Expected final online publication date for the Annual Review of Marine Science, Volume 13 is January 3, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

“…Microorganisms in the deep marine subsurface sediments represent a large unexplored biosphere, exploring and resolving their metabolisms are essential to understand the global biogeochemical cycles [59][60][61]. Despite the global importance of these microorganisms, deep-sea sediments are among the least understood environments, partly due to the difficulty of sampling as well as the complexity of inhabiting communities [59]. With this, the majority of deep-sea microbial diversity remains uncultured, hampering a more thorough understanding of their unique biology [3,59,62].…”

“…Despite the global importance of these microorganisms, deep-sea sediments are among the least understood environments, partly due to the difficulty of sampling as well as the complexity of inhabiting communities [59]. With this, the majority of deep-sea microbial diversity remains uncultured, hampering a more thorough understanding of their unique biology [3,59,62]. One of the striking characteristics of these uncultured lineages is that most of them are dominant population, for example, the large proportion of uncultured microbes was estimated to make up more than 75% of sediment genera [63].…”

Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology

“…Microbes in deep ocean sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes 24–26 . Despite the global importance of these microorganisms, majority of deep-sea microbial diversity remains uncultured and poorly characterized 24 . Description of the metabolisms of these novel taxa is advancing our understanding of their biogeochemical roles, including the coupling of elements and nutrient cycling, in the deep oceans.…”

Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

“…The application of culture-independent (CI) methods has transformed our understanding of microbial diversity while metagenome assembled genomes and single cell genomics have provided insight relevant to functional traits in yet to be cultured organisms (Kalisky and Quake, 2011;Evans et al, 2015;Parks et al, 2017). Despite these advances, the microbial diversity associated with marine sediments remains poorly characterized relative to other major biomes such as soil and seawater (Lloyd et al, 2018;Martiny, 2019;Baker et al, 2021). Sediment microbial communities are diverse (Thompson et al, 2017), densely populated, (Dale, 1974;Musat et al, 2006), play integral roles in fundamental ecosystem processes (Snelgrove et al, 1997;Baker et al, 2021), and can exhibit extraordinary levels of fine-scale spatial structure (Probandt et al, 2018).…”

“…Despite these advances, the microbial diversity associated with marine sediments remains poorly characterized relative to other major biomes such as soil and seawater (Lloyd et al, 2018;Martiny, 2019;Baker et al, 2021). Sediment microbial communities are diverse (Thompson et al, 2017), densely populated, (Dale, 1974;Musat et al, 2006), play integral roles in fundamental ecosystem processes (Snelgrove et al, 1997;Baker et al, 2021), and can exhibit extraordinary levels of fine-scale spatial structure (Probandt et al, 2018). While the inaccessibility of deep-sea sediments (>200 m depth) may contribute to the lack of data, the communities associated with shallow euphotic (£200 m depth) water sediments also remain poorly described (Baker et al, 2021).…”