Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has ...rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic ...expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H
), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H
and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H
and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H
oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.
The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes ...spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.
Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective ...remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.
•Pseudomonas and Rhodococcus are important oil degraders on high Arctic beaches.•Metagenomics detects oil degraders not previously found on high Arctic beaches.•Endemic microbial communities able to degrade hexadecane, naphthalene and alkanes•Nutrient biostimulation improves the biodegradation of hexadecane and naphthalene.
Global warming-induced sea ice loss in the Canadian Northwest Passage (NWP) will result in more shipping traffic, increasing the risk of oil spills. Microorganisms inhabiting NWP beach sediments may ...degrade hydrocarbons, offering a potential bioremediation strategy. In this study, the characterization and genomic analyses of 22 hydrocarbon-biodegradative bacterial isolates revealed that they contained a diverse range of key alkane and aromatic hydrocarbon-degradative genes, as well as cold and salt tolerance genes indicating they are highly adapted to the extreme Arctic environment. Some isolates successfully degraded Ultra Low Sulfur Fuel Oil (ULSFO) at temperatures as low as -5 °C and high salinities (3%-10%). Three isolates were grown in liquid medium containing ULSFO as sole carbon source over 3 months and variation of hydrocarbon concentration was measured at three time points to determine their rate of hydrocarbon biodegradation. Our results demonstrate that two isolates (
sp. R1B_2T and
sp. R2D_1T) possess complete degradation pathways and can grow on alkane and aromatic components of ULSFO under Arctic conditions. Overall, these results demonstrate that diverse hydrocarbon-degrading microorganisms exist in the NWP beach sediments, offering a potential bioremediation strategy in the events of a marine fuel spill reaching the shores of the NWP.
Hexabromocyclododecane (HBCD), a commonly used brominated flame retardant (BFR), has been listed as a persistent organic pollutant (POP). In order to remediate HBCD in the environment, the influence ...of microscale zerovalent iron (MZVI) on the HBCD degrading microcosm was evaluated. In the acclimated microcosm collected from river sediment, 49% of HBCD was initially removed through adsorption and then 30% of HBCD was biodegraded through non-debromination processes. In contrast to MZVI only, over 60% of HBCD was gradually degraded by MZVI through a debromination reaction. In the microcosm-MZVI combined system, the biodegradation ability of the microcosm was inhibited. The aqueous chemistry was changed by the addition of MZVI, which led to the alteration of microbial composition and biodegradation ability. These better understandings can facilitate an evaluation of the impact of MZVI on HBCD biodegradation when ZVI was used to remediate this BFR.
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•The influence of MZVI on the biodegradation of HBCD was first characterized.•A microcosm from sediment degraded HBCD through non-debromination process.•Co-incubation with MZVI inhibited the biodegradation ability of the microcosm.•The addition of MZVI altered water chemistry and microbial composition.•The negative effect of MZVI on microbial degradation of HBCD was observed.
•Six intermediates depict the metabolic pathways and the detoxification of BPA.•The novel BPA-degrading activity of Pseudomonas knackmussii is demonstrated.•The mixture of isolated strains enhances ...the BPA-degradation kinetics.•Microbial diversity is important for fast decomposition of the pollutant.
The wide distribution of bisphenol A (BPA) in the environment is problematic because of its endocrine-disrupting characteristics and toxicity. Developing cost-effective remediation methods for wide implementation is crucial. Therefore, this study investigated the BPA biodegradation ability of various microorganisms from river sediment. An acclimated microcosm completely degraded 10mgL−1 BPA within 28h and transformed the contaminant into several metabolic intermediates. During the degradation process, the microbial compositions fluctuated and the final, predominant microorganisms were Pseudomonas knackmussii and Methylomonas clara. From the original river sediment, we isolated four distinct strains, which deplete the BPA over 7–9 days. They were all genetically similar to P. knackmussii. The degradation ability of mixed strains was higher than that of single strain but was far less than that of the microbial consortium. The novel BPA degradation ability of P. knackmussii and its role in the decomposing microcosm were first demonstrated. Our results revealed that microbial diversity plays a crucial role in pollutant decomposition.
Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift ...between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H
) accumulates in silicate sand sediments due to decoupling of bacterial fermentation and respiration processes following anoxia. In situ measurements show that H
is 250-fold supersaturated in the water column overlying these sediments and has an isotopic composition consistent with fermentative production. Genome-resolved shotgun metagenomic profiling suggests that the sands harbour diverse and specialized microbial communities with a high abundance of NiFe-hydrogenase genes. Hydrogenase profiles predict that H
is primarily produced by facultatively fermentative bacteria, including the dominant gammaproteobacterial family Woeseiaceae, and can be consumed by aerobic respiratory bacteria. Flow-through reactor and slurry experiments consistently demonstrate that H
is rapidly produced by fermentation following anoxia, immediately consumed by aerobic respiration following reaeration and consumed by sulfate reduction only during prolonged anoxia. Hydrogenotrophic sulfur, nitrate and nitrite reducers were also detected, although contrary to previous hypotheses there was limited capacity for microalgal fermentation. In combination, these experiments confirm that fermentation dominates anoxic carbon mineralization in these permeable sediments and, in contrast to the case in cohesive sediments, is largely uncoupled from anaerobic respiration. Frequent changes in oxygen availability in these sediments may have selected for metabolically flexible bacteria while excluding strict anaerobes.
Lost Hammer Spring, located in the High Arctic of Nunavut, Canada, is one of the coldest and saltiest terrestrial springs discovered to date. It perennially discharges anoxic (<1 ppm dissolved ...oxygen), sub-zero (~-5 °C), and hypersaline (~24% salinity) brines from the subsurface through up to 600 m of permafrost. The sediment is sulfate-rich (1 M) and continually emits gases composed primarily of methane (~50%), making Lost Hammer the coldest known terrestrial methane seep and an analog to extraterrestrial habits on Mars, Europa, and Enceladus. A multi-omics approach utilizing metagenome, metatranscriptome, and single-amplified genome sequencing revealed a rare surface terrestrial habitat supporting a predominantly lithoautotrophic active microbial community driven in part by sulfide-oxidizing Gammaproteobacteria scavenging trace oxygen. Genomes from active anaerobic methane-oxidizing archaea (ANME-1) showed evidence of putative metabolic flexibility and hypersaline and cold adaptations. Evidence of anaerobic heterotrophic and fermentative lifestyles were found in candidate phyla DPANN archaea and CG03 bacteria genomes. Our results demonstrate Mars-relevant metabolisms including sulfide oxidation, sulfate reduction, anaerobic oxidation of methane, and oxidation of trace gases (H
, CO
) detected under anoxic, hypersaline, and sub-zero ambient conditions, providing evidence that similar extant microbial life could potentially survive in similar habitats on Mars.
Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial ...metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.
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•Diesel exposure reduces microbial diversity in Arctic beach sediments•Selection for the Psychrobacter genus at higher diesel concentrations•Nutrients help maintain microbial activity when sediment is exposed to marine diesel•Diesel enriched for phenylalanine metabolism & malate synthesis microbial functions•Diesel selected for microorganisms with (an)aerobic hydrocarbon degradation potential
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