Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater

Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.

Composition of microorganisms in carbonated mineral waters of the Mukhen deposit (Khabarovsk territory)

The chemical composition, distribution, structure, number of physiological groups of cultivated bacteria and their biodiversity in the cold carbonic mineral waters of Mukhen and in microbial mats were studied. It is shown that the mineral waters are cold, hydrocarbonate-calcium-magnesium, enriched with iron, manganese, barium. Carbon dioxide predominates in the gaseous composition of waters. Microbiological studies have shown that no sanitary-indicative microflora was found in mineral waters, which indicates the purity of underground waters. Carbonic waters were characterized by a low number of physiological groups of autochthonous bacteria. Among the studied microorganisms, chemolithotrophic thionic bacteria predominated, which indicates the predominance of oxidation processes of reduced sulfur compounds with the participation of bacteria in groundwater. In the microbial mats, various chemolithotrophic and heterotrophic microorganisms were identified, participating in the geochemical cycles of carbon, nitrogen, sulfur, iron, manganese, and silicon. The number of physiological groups of bacteria was higher than in mineral waters, along with this saprophytic bacteria predominated significantly. A sufficiently high rate of protein and cellulose decomposition by microorganisms of microbial mats was shown. A low diversity of cultured heterotrophic bacteria with the dominance of microorganisms of the genus Bacillus was found in mineral waters and in microbial mats. By using the methods of X-ray phase analysis, the important role of microorganisms of microbial mats in the precipitation of silicate minerals and the formation of calcium carbonates was shown.

Gaseous pollutants from a small-scale aerobic biological treatment facility: odor and health risk assessment

Background Biological treatment technology is good for the recovery of resources and energy from municipal solid waste (MSW) and cutting down biodegradable components in landfill waste. Recently, the aerobic biological treatment of MSW has increased in rural areas of China. These facilities are usually open setup and close to nearby residents, and complaints tend to be received regarding odorous gases. A semi-in-vessel setup facility was built in recent years, and its impact on the environment and personnel is not clear. Results Ammonia was the predominant compound released from the windrow and its concentration was one order of magnitude higher than those of other compounds. Terpenes and reduced sulfur compounds (RSCs) persisted throughout the entire active fermentation process, with only slight decreases. The biofilter pool had a greater odor impact on the surrounding neighborhood than the waste unloading and sorting operation. The concentrations of most compounds were reduced by the biofilter pool. Ten major substances that caused odors at the facility were analyzed, where most comprised RSCs. The odor impact of the facility was low, but it was associated with a carcinogenic risk to the operators, thereby indicating the need to improve personal protection. Conclusions Large amounts of ammonia and volatile organic compounds were released from the composting units, but they had a low odor impact on the environment because of the semi-in-vessel setup. The odor impact of the facility was low but it was associated with a carcinogenic risk to the operators. This technology can be popularized in rural areas.

Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

Effects of combined tannic acid/fluoride on sulfur transformations and methanogenic pathways in swine manure

Livestock manure emits reduced sulfur compounds and methane, which affect nature and the climate. These gases are efficiently mitigated by addition of a tannic acid-sodium fluoride combination inhibitor (TA-NaF), and to some extent by acidification. In this paper, TA-NaF treatment was performed on swine manure to study the treatment influence on methanogenic pathways and sulfur transformation pathways in various laboratory experiments. Stable carbon isotope labeling revealed that both untreated and TA-NaF treated swine manures were dominated by hydrogenotrophic methanogenesis. However, in supplementary experiments in wastewater sludge, TA-NaF clearly inhibited acetoclastic methanogenesis, whereas acidification inhibited hydrogenotrophic methanogenesis. In swine manure, TA-NaF inhibited s-amino acid catabolism to a larger extent than sulfate reduction. Conversely, acidification reduced sulfate reduction activity more than s-amino acid degradation. TA-NaF treatment had no significant effect on methanogenic community structure, which was surprising considering clear effects on isotope ratios of methane and carbon dioxide. Halophile sulfate reducers adapted well to TA-NaF treatment, but the community change also depended on temperature. The combined experimental work resulted in a proposed inhibition scheme for sulfur transformations and methanogenic pathways as affected by TA-NaF and acidification in swine manure and in other inocula.

Acidity and sulfur oxidation intermediate concentrations controlled by O2-driven partitioning of sulfur oxidizing bacteria in a mine tailings impoundment

Acidification of freshwater in mining impacted areas is a major global environmental problem catalyzed by sulfur-oxidizing bacteria (SOB). To date, little is known about the active bacteria in mine tailings impoundments and their environmental niches. Here, biological sulfur oxidation was investigated over four years in a mine tailings impoundment, integrating sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. We demonstrated oxygen driven niche partitioning of SOB and their metabolic pathways that explain acidity generation and thiosulfate persistence. Four chemolithoautotrophic SOB, Halothiobacillus, Thiobacillus, Sulfuricurvum and Sediminibacterium comprised 37% to 73% of the analyzed communities. The impoundment waters alternated between the dominance of Halothiobacillus versus a Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium consortia. Halothiobacillus dominance was associated with lower pH values (~4.3), higher [H+]/[SO42-] and lower [S2O32-], collectively indicative of extensive sulfur oxidation. Halothiobacillus, which couple sulfur oxidation via the Sox pathway to aerobic respiration or NO2- reduction, were present throughout the depth profile, yet their expression of sox genes occurred only in upper highly oxygenated waters. Conversely, when consortia of Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium dominated, recycling/disproportionating reactions were more prevalent. Thiobacillus, which dominated deeper micro-oxic/anoxic waters, oxidized sulfur primarily through the rDSR pathway, coupled to NO3-/NO2- reduction, resulting in lower [H+]/[SO42-] and higher [S2O32-] relative to upper waters. These field results mirror the Sox/rDSR-geochemical patterns of experimental SOB enrichments and reveal opportunities for biological treatments of recalcitrant reduced sulfur compounds, as well as gene-based monitoring and in situ RNA detection to predict the onset of problematic geochemistry.

Gaseous Pollutants From A Small-Scale Aerobic Biological Treatment Facility: Odor And Carcinogenic Risk Assessment

BACKGROUND: Biological treatment technology is good for the recovery of resources and energy from municipal solid waste (MSW) and cutting down biodegradable components in landfill waste. Recently, the aerobic biological treatment of MSW has increased in rural areas of China. These facilities are usually open setup and closed to nearby residents, and complaints tend to be received regarding odorous gases. A semi-in-vessel setup facility was occured in recent years, and its impact on the environment and personnel is not clear.RESULTS: Ammonia was the predominant compound released from the windrow and its concentration was one order of magnitude higher than those of other compounds. Terpenes and reduced sulfur compounds (RSCs) persisted throughout the entire active fermentation process, with only slight decreases. The biofilter pool had a greater odor impact on the surrounding neighborhood than the waste unloading and sorting operation. The concentrations of most compounds were reduced by the biofilter pool. Ten major substances that caused odors at the periphery of the facility were analyzed, where most comprised RSCs. The odor impact of the facility was low but it was associated with a carcinogenic risk to the operators, thereby indicating the need to improve personal protection.Conclusions: Large amounts of ammonia and volatile organic compounds were released from the composting units, but they had a low odor impact on the environment because of the semi-in-vessel setup. The odor impact of the facility was low but it was associated with a carcinogenic risk to the operators. This technology can be popularized in rural areas.

“Candidatus Chlorobium masyuteum,” a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake

Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. “Candidatus Chlorobium masyuteum” grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe “Candidatus Pseudopelobacter ferreus” is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While “Ca. C. masyuteum” is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day–1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.

Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide

Hydrogen sulfide is a toxic compound that can affect various groups of water microorganisms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as well as the conditions for isolation and cultivation of these microorganisms will be presented.