Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide

Abstract

23Bacteria within aerated environments often exist within a variety of dormant forms. In 24 these states, bacteria endure adverse environmental conditions such as organic 25 carbon starvation by decreasing metabolic expenditure and using alternative energy 26 sources. In this study, we investigated the energy sources that facilitate the 27 persistence of the environmentally widespread but understudied bacterial phylum 28 Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class 29 Chloroflexia) extensively remodels its respiratory chain upon entry into stationary 30 phase due to organic carbon limitation. Whereas primary dehydrogenases associated 31 with heterotrophic respiration were downregulated, putative operons encoding 32 enzymes involved in molecular hydrogen (H2), carbon monoxide (CO), and sulfur 33 compound oxidation were significantly upregulated. Gas chromatography and 34 microsensor experiments were used to show that T. roseum aerobically respires H2 35 and CO at a range of environmentally relevant concentrations to sub-atmospheric 36 levels. Phylogenetic analysis suggests that the enzymes mediating atmospheric H2 37 and CO oxidation, namely group 1h [NiFe]-hydrogenases and type I carbon monoxide 38 dehydrogenases, are widely distributed in Chloroflexi genomes and have been 39 acquired on at least two occasions through separate horizontal gene transfer events. 40Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 41(class Ktedonobacteria) also oxidises atmospheric H2 and CO during persistence. This 42 study provides the first axenic culture evidence that atmospheric CO supports bacterial 43 persistence and reports the third phylum to be experimentally shown to mediate the 44 biogeochemically and ecologically important process of atmospheric H2 oxidation. This 45 adds to the growing body of evidence that atmospheric trace gases serve as 46 dependable energy sources for the survival of dormant microorganisms. 47 48 49 Bacteria from the phylum Chloroflexi are widespread and abundant in free-living 50 microbial communities [1-4]. One reason for their success is their metabolic diversity; 51 cultured strains from the phylum include heterotrophs, lithotrophs, and phototrophs 52 adapted to both oxic and anoxic environments [5]. Cultured representatives of the 53 phylum are classified into four classes by the genome taxonomy database [6], the 54 primarily aerobic Chloroflexia and Ktedonobacteria and the anaerobic Anaerolineae 55 and Dehalococcoidia [5]. Numerous studies have provided insight into the metabolic 56 strategies anaerobic classes within Chloroflexi use to adapt to oligotrophic niches [7, 57 8]. Surprisingly little, however, is known about how aerobic heterotrophic bacteria 58 within this phylum colonise oxic environments. Global surveys have reported that 59 Chloroflexi comprise 4.3% of soil bacteria [2] and 3.2% of marine bacteria [3]. However, 60 the most dominant lineages within these ecosystems (notably Ellin6524 and SAR202) 61 have proven...

Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics

“…Currently, there are 188 draft genomes with more than 90% completeness deposited in the NCBI database as of May 2019 1 and 546 genomes (>50% complete and <10% contamination) are listed in the Genome Taxonomy Database (GTDB) (Parks et al, 2018). Interestingly, Chloroflexi isolates exhibit a broad diversity of phenotypes and a wide range of metabolic activities (Hug et al, 2013;Islam et al, 2019) and are often found as important members in the environment (Hanada et al, 2002;Taş et al, 2009;Chang et al, 2011;McIlroy et al, 2016;Livingstone et al, 2018). However, as the numbers show they are apparently difficult to cultivate.…”

Cryptogams signify key transitions of bacteria and fungi in Arctic sand dune succession

“…A characteristic bacterial group for the early stages from bare sand to lichen was candidate phylum WD272, currently known as WPS‐2 and recently named Candidatus Eremiobacterota, ‘desert bacterial phylum’, which are proposed to be autotrophs able to use atmospheric H 2 and carbon monoxide (CO) as energy sources (Ji et al , ; Holland‐Moritz et al , ). Another potential H 2 ‐ and CO‐oxidising bacterial group in the moss and lichen stages was members of Chloroflexi classified as Ktedonobacteria (King & King, ; Islam et al , ). The increased occurrence of WD272 and Chloroflexi in the moss and lichen stages suggests that they may form a basis of biomass accumulation in the Arctic sand dune succession.…”

Technical Note: Inexpensive modification of Exetainers for the reliable storage of trace-level hydrogen and carbon monoxide gas samples

“…The level of contamination was proportional to the volume of the vial and the mass of rubber (a proxy for the specific surface area in contact with the enclosed gas phase); therefore, form factor and volume of vials have to be considered. For example, serum vials with an increased volume of >100 mL and thus lower exposed surface area relative to volume may still be suitable for gas storage or incubation experiments lasting a few weeks, if treated stoppers are used (Islam et al, 2019(Islam et al, , 2020Kessler et al, 2019).…”

“…Samples were then measured 5 times over the course of 9 days; samples were measured repeatedly, except for 3 mL control Exetainers which were discarded after measurements due to insufficient volume for repeated sampling. Measurements of H 2 , CO and CH 4 were performed on a VICI TGA 6k equipped with an autosampler and a sample-injection loop of 1 mL, using a pulse-discharge helium ionisation detector as described earlier (Islam et al, 2019). The detection limits for the three gases were 61 ppb for H 2 , 10 ppb for CO and 170 ppb for CH 4 as determined by replicate samples (n=7) of zero-grade air zero (BOC Australia, North Ryde NSW, Australia).…”