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

Abstract

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...

Atribacteria reproducing over millions of years in the Atlantic abyssal subseafloor

“…Moreover, in culture experiments from the first cultivated representative of the Atribacteria, the presence of an H2-consuming methanogenic partner increased the growth rate of Atribacteria by more than 100 fold (43). Based on this experimental result, we speculate that the relatively high abundance of the Atribacteria in our sampled ancient anoxic sediment could be attributed to an as-of-yet unidentified syntrophic or semi-syntrophic partner organism, from the Chloroflexi, for example Dehalococcoidia (74,75).…”

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

“…Moreover, in culture experiments from the first cultivated representative of the atribacteria, the presence of an H 2 -consuming methanogenic partner increased the growth rate of atribacteria by more than 100-fold (43). Based on this experimental result, we speculate that the relatively high abundance of the atribacteria in our sampled ancient anoxic sediment could be attributed to an as-of-yet-unidentified syntrophic or semisyntrophic partner organism, from the Chloroflexi, for example, Dehalococcoidia (74,75).…”

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

“…Similarly, Anaerolineae (Chloroflexi) , which constituted a significant portion of the deep anoxic microbial community (14%) (Figure 5), benefit from the hydrogen‐producing bacteria. Even though the members of this genus are typically photoautotrophs and photoheterotrophs, they are capable of growing in the dark using hydrogen and H 2 S as electron donors, and a wide variety of organic substances, such as sugars or amino acids, as carbon source (Vuillemin et al, 2020).…”