Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments

FEMS Microbiology Ecology

Kerrigan

Dhondt

et al. 2020

Chloroflexi are widespread in subsurface environments, and recent studies indicate that they represent a major fraction of the communities in subseafloor sediment. Here, we compare the abundance, diversity, metabolic potential, and gene expression of Chloroflexi from three abyssal sediment cores from the western North Atlantic Gyre (water depth >5400 m) covering up to 15 million years of sediment deposition, where Chloroflexi were found to represent major components of the community at all sites. Chloroflexi communities die off in oxic red clay over 10 to 15 million years, and gene expression was below detection. In contrast, Chloroflexi abundance and gene expression at the anoxic abyssal clay site increase below the seafloor and peak in 2 to 3 million-year-old sediment, indicating a comparably higher activity. Metatranscriptomes from the anoxic site reveal increased expression of Chloroflexi genes involved in cell wall biogenesis, protein turnover, inorganic ion transport, defense mechanisms and prophages. Phylogenetic analysis shows that these Chloroflexi are closely related to homoacetogenic subseafloor clades and actively transcribe genes involved in sugar fermentations, gluconeogenesis and Wood-Ljungdahl pathway in the subseafloor. Concomitant expression of cell division genes indicates that these putative homoacetogenic Chloroflexi are actively growing in these million-year-old anoxic abyssal sediments.

Section: Resultsmentioning

confidence: 99%

Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay

FEMS Microbiology Ecology

Kerrigan

Dhondt

et al. 2020

“…According to a protocol for quantitative normalization of barcoded 16S gene sequence data ( 24 ), we normalized group-specific 16S rRNA gene abundances by dividing the total number of 16S rRNA gene copies determined via quantitative PCR (qPCR) by their affiliated 16S rRNA gene relative abundances (fractional percentage of total sequences per sample). This showed that “ Ca .…”

Section: Resultsmentioning

confidence: 99%

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

Vargas

Coskun

et al. 2020

mBio

How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum “Candidatus Atribacteria,” which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. “Ca. Atribacteria” dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing “Ca. Atribacteria” also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD+. Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor “Ca. Atribacteria,” as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the “Ca. Atribacteria” can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments. IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum “Candidatus Atribacteria” dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that “Ca. Atribacteria” can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.

“…At oxic site 12, our limit of detection (10 2 × 16S rRNA gene copies per DNA extraction) is reached at ~8 mbsf, whereas at oxic site 11, the density of 16S rRNA genes increases by two orders of magnitude at ~6 mbsf before reaching the detection limit at 15 mbsf. Similar to the procedure described by Lloyd et al (2020), we normalized the fractional abundance of the Chloroflexi 16S rRNA abundance to quantitative values using the qPCR determined 16S rRNA gene concentrations as described previously (Vuillemin et al, 2019). The 16S rRNA gene density of Chloroflexi at both oxic sites sampled decreases constantly with depth, reaching the limit of detection at 15 mbsf at site 11 and at mbsf at site 12.…”

Section: Diversity Density and Taxonomy Of 16s Rrna Genesmentioning

confidence: 99%

Chloroflexi persisting for millions of years in oxic and anoxic deep-sea clay

Kerrigan

Dhondt

et al. 2020

Preprint

Significance statement: Chloroflexi are widespread in energy-limited subseafloor sediments, both in 29 oxic subseafloor sediments that are energetically limited by the availability of electron donors (organic 30 matter) and in anoxic sediments that are energetically limited by the availability of high energy terminal 31 electron acceptors. How Chloroflexi respond to these different forms of energy limitation over long time 32 scales is poorly understood. We present new data that demonstrates how key differences in metabolism 33 are manifested in different communities of aerobic and anaerobic Chloroflexi subsisting over millions of 34 years in oxic and anoxic deep-sea clay. These data provide new insights into how certain Chloroflexi 35 respond to different types of long-term energy limitation.36 2 Abstract 37 Chloroflexi are widespread in energy-limited subseafloor sediments, but how Chloroflexi respond to 38 subseafloor energy limitation under oxic and anoxic conditions is poorly understood. Here, we 39 characterize the diversity, abundance, activity, and metabolic potential of Chloroflexi in oxic and anoxic 40 abyssal clay from three deep-sea cores covering up to 15 million years of sediment deposition, where 41 Chloroflexi are a major component of the community throughout the entire cored sequence at all sites. 42 In oxic red clay at two different sites, Chloroflexi communities exhibit net death over both 10-15 million 43 year cored sequences, and gene expression was below detection despite the availability of oxygen as a 44 high energy electron acceptor, indicating a reduced level of activity. In contrast at the anoxic site, 45 Chloroflexi abundance and gene expression increase below the seafloor and peak in 2 to 3 million year 46 old sediment. The anaerobic subseafloor Chloroflexi exhibited a homoacetogenic metabolism and 47 potential for energetically efficient intracellular H 2 recycling that have been proposed to confer a fitness 48 advantage in energy-limited subseafloor habitats. Our findings indicate that the expression of this 49 energy efficient metabolism in Chloroflexi coincides with net growth over million year timescales in 50 deep-sea anoxic clay. 51 52 54 sediment deposition per million years in abyssal regions (D'Hondt et al., 2015) and most organic flux to 55 the sediment is consumed before it can be buried (Røy et al., 2012). As a result, microbial communities 56 in abyssal subseafloor sediment are characterized by extremely low cell densities (Kallmeyer et al., 57 2012), experience extreme energy limitation over the long term (Hoehler and Jørgensen, 2013), even 58 over million year timescales under both oxic and anoxic conditions (D'Hondt et al., 2015). The 59 sedimentary material of the deep-sea is characterized by ultra-small (<0.2 µm) clay particles that are 60 3highly pressurized under the >5,000 m of overlying seawater, which likely hinders the motility of cells 61 in this extreme environment, resulting in a complete separation from the surface after deposition. 62Cells subsisting in d...