Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades

Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation

Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.

Campylobacterota dominate the microbial communities in a tropical karst subterranean estuary, with implications for cycling and export of nitrogen to coastal waters

Subterranean estuaries (STEs), the zones in which seawater and subsurface groundwater mix, are recognized as hotspots for biogeochemical reactions; however, little is known of the microbial communities that control many of those reactions. This study investigated the potential functions of microbes inhabiting a cenote and an offshore submarine spring (Pargos) in the near-coastal waters of the Yucatan Peninsula, Mexico. The inland cenote (Cenote Siete Bocas; C7B) is characterized by a chemocline that is host to an array of physicochemical gradients associated with microbial activities. The chemocline includes an increasing gradient in sulfide concentrations with depth and a decreasing gradient in nitrate concentrations. The microbial community within the chemocline was dominated by Sulfurimonas and Sulfurovum of the Campylobacteria, which are likely responsible for sulfide oxidation coupled with nitrate reduction. Although C7B has not been directly connected with Pargos Spring, water discharging from the spring has physicochemical characteristics and microbial community structures similar to C7B, strongly suggesting biogeochemical processing in the STE impacts groundwater composition prior to discharge. This work yields insight into the microbial communities and biogeochemical reactions in STEs in karstic aquifers and provides evidence for the importance of Campylobacteria in controlling nitrate concentrations exported to marine springs.

Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs

Freshwater reservoirs emit greenhouse gases (GHGs) such as methane (CH₄) and carbon dioxide (CO₂), contributing to global warming, mainly when impacted by untreated sewage and other anthropogenic sources. These gases can be produced by microbial organic carbon decomposition, but little is known about the microbiota and its participation in GHG production and consumption in these environments. In this paper we analyzed the sediment microbiota of three eutrophic tropical urban freshwater reservoirs, in different seasons and evaluated the correlations between microorganisms and the atmospheric CH₄ and CO₂ flows, also correlating them to limnological variables. Our results showed that deeper water columns promote high methanogen abundance, with predominance of acetoclastic Methanosaeta spp. and hydrogenotrophs Methanoregula spp. and Methanolinea spp. The aerobic methanotrophic community was affected by dissolved total carbon (DTC) and was dominated by Crenothrix spp. However, both relative abundance of the total methanogenic and aerobic methanotrophic communities in sediments were uncoupled to CH₄ and CO₂ flows. Network based approach showed that fermentative microbiota, including Leptolinea spp. and Longilinea spp., which produces substrates for methanogenesis, influence CH₄ flows and was favored by anthropogenic pollution, such as untreated sewage loads. Additionally, less polluted conditions favored probable anaerobic methanotrophs such as Candidatus Bathyarchaeota, Sva0485, NC10, and MBG-D/DHVEG-1, which promoted lower gaseous flows, confirming the importance of sanitation improvement to reduce these flows in tropical urban freshwater reservoirs and their local and global warming impact.

Mercury methylation in rice paddy and accumulation in rice plant: A review

The bioavailability and toxicity of mercury (Hg) are dependent on its chemical speciation, in which methylmercury (MeHg) is the most toxic compound. Inorganic Hg can be transformed into MeHg in anaerobic conditions. Subsequent accumulation and biomagnification in the food chain pose a potential threat to human health. Previous studies have confirmed that paddy soil is an important site for MeHg production, and rice fields are an important source of MeHg in terrestrial ecosystems. Rice (Oryza sativa L.) is recently confirmed as a potential bioaccumulator plant of MeHg. Understanding the behaviour of Hg in rice paddies is important, particularly the mechanisms involved in Hg sources, uptake, toxicity, detoxification, and accumulation in crops. This review highlights the issue of MeHg-contaminated rice, and presents the current understanding of the Hg cycling in the rice paddy ecosystem, including the mechanism and processes of Hg species accumulation in rice plants and Hg methylation/demethylation processes in rice paddies and the primary controlling factors. The review also identified various research gaps in previous studies and proposes future research objectives to reduce the impact of Hg-contamination in rice crops.

Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄ )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

Shifts in mercury methylation across a peatland chronosequence: From sulfate reduction to methanogenesis and syntrophy

Peatlands are globally important ecosystems where inorganic mercury is converted to bioaccumulating and highly toxic methylmercury, resulting in high risks of methylmercury exposure in adjacent aquatic ecosystems. Although biological mercury methylation has been known for decades, there is still a lack of knowledge about the organisms involved in mercury methylation and the drivers controlling their methylating capacity. In order to investigate the metabolisms responsible for mercury methylation and methylmercury degradation as well as the controls of both processes, we studied a chronosequence of boreal peatlands covering fundamentally different biogeochemical conditions. Potential mercury methylation rates decreased with peatland age, being up to 53 times higher in the youngest peatland compared to the oldest. Methylation in young mires was driven by sulfate reduction, while methanogenic and syntrophic metabolisms became more important in older systems. Demethylation rates were also highest in young wetlands, with a gradual shift from biotic to abiotic methylmercury degradation along the chronosequence. Our findings reveal how metabolic shifts drive mercury methylation and its ratio to demethylation as peatlands age.

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

BACKGROUND

Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).

METHODS

Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.

RESULTS

The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.

CONCLUSION

This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.

Periphyton and Flocculent Materials Are Important Ecological Compartments Supporting Abundant and Diverse Mercury Methylator Assemblages in the Florida Everglades

Mercury (Hg) methylation in the Florida Everglades is of great environmental concern because of its adverse effects on human and wildlife health through biomagnification in aquatic food webs. Periphyton and flocculant materials (floc) overlaying peat soil are important ecological compartments producing methylmercury (MeHg) in this ecosystem. These compartments retain higher concentrations of MeHg than did soil at study sites across nutrient and/or sulfate gradient(s). To better understand what controls Hg methylation in these compartments, the present study explored the structures and abundances of Hg methylators using genes hgcAB as biomarkers. The hgcA sequences indicated that these compartments hosted a high diversity of Hg methylators, including Deltaproteobacteria, Chloroflexi, Firmicutes, and Methanomicrobia, with community compositions that differed between these habitats. The copy numbers of hgcAB quantified by quantitative PCR revealed that floc and soil supported higher numbers of Hg methylators than periphyton in the Everglades ecosystem. The abundance of Hg methylators was strongly positively correlated with concentrations of carbon and nutrients (e.g., phosphorus and nitrogen) according to redundancy analysis. Strong correlations were also observed among numbers of sulfate reducers, methanogens, and the dominant hgcAB-carrying groups, suggesting that hgcAB would spread primarily through the growth of those assemblages. The abundances of Hg methylators were weakly negatively correlated to MeHg concentrations, suggesting that the size of this population would not solely determine the final concentrations of MeHg in the ecological compartments studied. This study extends the knowledge regarding the distribution of diverse potential mercury methylators in different environmental compartments in a wetland of national concern.IMPORTANCE Methylmercury is a potent neurotoxin that impacts the health of humans and wildlife. Most mercury in wetlands such as the Florida Everglades enters as inorganic mercury via atmospheric deposition, some of which is transformed to the more toxic methylmercury through the activities of anaerobic microorganisms. We investigated the numbers and phylogenetic diversity of hgcAB, genes that are linked to mercury methylation, in the soil, floc, and periphyton in areas of the Everglades with different sulfate and nutrient concentrations. Soil harbored relatively high numbers of cells capable of methylating mercury; however, little detectable methylmercury was present in soil. The greatest concentrations of methylmercury were found in floc and periphyton. The dominant methylators in those compartments included methanogens and Syntrophobacteriales This work provides significant insight into the microbial processes that control methylation and form the basis for accumulation through the food chain in this important environment.

Effects of molybdenum, selenium and manganese supplementation on the performance of anaerobic digestion and the characteristics of bacterial community in acidogenic stage

The addition of trace elements to aid anaerobic digestion has already been widely studied. However, the effects of rare trace elements on anaerobic digestion remain unclear. In this study, the effects of Mo, Se and Mn on anaerobic digestion of rice straw were explored. The results showed the methane yield increased by 59.3%, 47.1% and 48.9% in the first 10 days following addition of Mo (0.01 mg/L), Se (0.1 mg/L) and Mn (1.0 mg/L), respectively. Toxic effects and the accumulation of volatile fatty acids (VFAs) were observed when the Se, Mo and Mn concentrations were greater than 100, 1000 and 1000 mg/L, respectively. The half-maximal inhibitory concentrations (IC₅₀) for Se, Mn and Mo were 79.9 mg/L, 773.9 mg/L and 792.3 mg/L, respectively. The addition of trace elements has changed the bacterial structure of the bacteria, which in turn has affected the digestion performance.

Methanogens Are Major Contributors to Nitrogen Fixation in Soils of the Florida Everglades

The objective of this study was to investigate the interaction of the nitrogen (N) cycle with methane production in the Florida Everglades, a large freshwater wetland. This study provides an initial analysis of the distribution and expression of N-cycling genes in Water Conservation Area 2A (WCA-2A), a section of the marsh that underwent phosphorus (P) loading for many years due to runoff from upstream agricultural activities. The elevated P resulted in increased primary productivity and an N limitation in P-enriched areas. Results from quantitative real-time PCR (qPCR) analyses indicated that the N cycle in WCA-2A was dominated by nifH and nirK/S, with an increasing trend in copy numbers in P-impacted sites. Many nifH sequences (6 to 44% of the total) and nifH transcript sequences (2 to 49%) clustered with the methanogenic Euryarchaeota, in stark contrast to the proportion of core gene sequences representing Archaea (≤0.27% of SSU rRNA genes) for the WCA-2A microbiota. Notably, archaeal nifH gene transcripts were detected at all sites and comprised a significant proportion of total nifH transcripts obtained from the unimpacted site, indicating that methanogens are actively fixing N₂ Laboratory incubations with soils taken from WCA-2A produced nifH transcripts with the production of methane from H₂ plus CO₂ and acetate as electron donors and carbon sources. Methanogenic N₂ fixation is likely to be an important, although largely unrecognized, route through which fixed nitrogen enters the anoxic soils of the Everglades and may have significant relevance regarding methane production in wetlands.IMPORTANCE Wetlands are the most important natural sources of the greenhouse gas methane, and much of that methane emanates from (sub)tropical peatlands. Primary productivity in these peatlands is frequently limited by the availability of nitrogen or phosphorus; however, the response to nutrient limitations of microbial communities that control biogeochemical cycling critical to ecosystem function may be complex and may be associated with a range of processes, including methane production. We show that many, if not most, of the methanogens in the peatlands of the Florida Everglades possess the nifH gene and actively express it for N₂ fixation coupled with methanogenesis. These findings indicate that archaeal N₂ fixation would play crucial role in methane emissions and overall N cycle in subtropical wetlands suffering N limitation.

Vertical gradients in carbon flow and methane production in a sulfate-rich oil sands tailings pond

Oil sands tailings ponds are primary storage basins for tailings produced during oil sands processing in Alberta (Canada). Due to microbial metabolism, methane production contributes to greenhouse gas emissions, but positively affects tailings densification, which is relevant for operational water re-use. Depending on the age and depth of tailings, the activity of sulfate-reducing bacteria (SRB) may control methanogenesis due to the competition for substrates. To assess the depth-related impact of sulfate reduction on CH₄ emissions, original tailings of two vicinal pond profiles were incubated in anoxic microcosms with/without molybdate as selective inhibitor of microbial sulfate reduction. Integrating methane production rates, considerable volumes of CH₄ emissions (∼5.37 million L d^-1) may be effectively prevented by the activity of SRB in sulfidic tailings between 3.5 and 7.5 m. To infer metabolic potentials controlling methanogenic pathways, a set of relevant organic acids (acetate, formate, propionate, butyrate, lactate) was added to part of the microcosms. Generally, organic acid transformation shifted with depth, with highest rates (305-446 μmol L^-1 d^-1) measured in fresh tailings at 5.5-7.5 m. In all depths, a transient accumulation of acetate revealed its importance as key intermediate during organic matter decomposition. SRB dominated the transformation of acetate, butyrate and propionate, but were not essential for lactate and formate turnover. Acetate as methanogenic substrate was important only at 13.5 m. At 1-7.5 m, methanogenesis significantly increased in presence of organic acids, most likely due to the syntrophic oxidation of acetate to CO₂ by SRB and subsequent conversion to CH₄.