Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Mixed nitrate and metal contamination influences operational speciation of toxic and essential elements

Environmental contamination constrains microbial communities impacting diversity and total metabolic activity. The former S-3 Ponds contamination site at Oak Ridge Reservation (ORR), TN, has elevated concentrations of nitric acid and multiple metals from decades of processing nuclear material. To determine the nature of the metal contamination in the sediment, a three-step sequential chemical extraction (BCR) was performed on sediment segments from a core located upgradient (EB271, non-contaminated) and one downgradient (EB106, contaminated) of the S-3 Ponds. The resulting exchangeable, reducing, and oxidizing fractions were analyzed for 18 different elements. Comparison of the two cores revealed changes in operational speciation for several elements caused by the contamination. Those present from the S-3 Ponds, including Al, U, Co, Cu, Ni, and Cd, were not only elevated in concentration in the EB106 core but were also operationally more available with increased mobility in the acidic environment. Other elements, including Mg, Ca, P, V, As, and Mo, were less operationally available in EB106 having decreased concentrations in the exchangeable fraction. The bioavailability of essential macro nutrients Mg, Ca, and P from the two types of sediment was determined using three metal-tolerant bacteria previously isolated from ORR. Mg and Ca were available from both sediments for all three strains; however, P was not bioavailable from either sediment for any strain. The decreased operational speciation of P in contaminated ORR sediment may increase the dependence of the microbial community on other pools of P or select for microorganisms with increased P scavenging capabilities. Hence, the microbial community at the former S-3 Ponds contamination site may be constrained not only by increased toxic metal concentrations but also by the availability of essential elements, including P.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Mixed heavy metal stress induces global iron starvation response

Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

Micronutrients in Food Production: What Can We Learn from Natural Ecosystems?

Soil micronutrients limit crop productivity in many regions worldwide, and micronutrient deficiencies affect over two billion people globally. Microbial biofertilizers could combat these issues by inoculating arable soils with microorganisms that mobilize micronutrients, increasing their availability to crop plants in an environmentally sustainable and cost-effective manner. However, the widespread application of biofertilizers is limited by complex micronutrient–microbe–plant interactions, which reduce their effectiveness under field conditions. Here, we review the current state of seven micronutrients in food production. We examine the mechanisms underpinning microbial micronutrient mobilization in natural ecosystems and synthesize the state-of-knowledge to improve our overall understanding of biofertilizers in food crop production. We demonstrate that, although soil micronutrient concentrations are strongly influenced by soil conditions, land management practices can also substantially affect micronutrient availability and uptake by plants. The effectiveness of biofertilizers varies, but several lines of evidence indicate substantial benefits in co-applying biofertilizers with conventional inorganic or organic fertilizers. Studies of micronutrient cycling in natural ecosystems provide examples of microbial taxa capable of mobilizing multiple micronutrients whilst withstanding harsh environmental conditions. Research into the mechanisms of microbial nutrient mobilization in natural ecosystems could, therefore, yield effective biofertilizers to improve crop nutrition under global changes.

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment

Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment.

Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation in Tennessee. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment.

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (K_D) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [K_D (Mo) 27.0 nM, K_D (W) 26.7 nM] and E. coli K12[(K_D (Mo) 25.0 nM, K_D (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

Contribution of autochthonous diazotrophs to polycyclic aromatic hydrocarbon dissipation in contaminated soils

Understanding the role played by autochthonous functional microbes involved in the biotransformation of pollutants would help optimize bioremediation performance at contaminated sites. However, our knowledge of the remediation potential of indigenous diazotrophs in contaminated soils remains inadequate. Using a microcosm experiment, soil nitrogen fixation activity was manipulated by molybdenum (Mo) and tungsten (W), and their effect on the removal of polycyclic aromatic hydrocarbons (PAHs) was determined in agricultural and industrial soils. Results showed that after 42 days of incubation, PAH dissipation efficiency was significantly enhanced by 1.06-fold in 600 μg kg^-1 Mo-treated agricultural soil, compared with that in the control. For the industrial soil, 1200 μg kg^-1 Mo treatment significantly promoted PAH removal by 90.76% in 21 days, whereas no significant change was observed between treatments and control at the end of the incubation period. W also exerted a similar effect on PAH dissipation. The activity and gene abundance of nitrogenase were also increased under Mo/W treatments in the two soils. Spearman's correlation analysis further indicated that removal of PAHs was positively correlated with nitrogenase activity in soil, which could be due to the elevated abundances of PAH-degrading genes (PAH-RHDα) in these treatments. Our results suggest the importance of autochthonous diazotrophs in PAH-contaminated soils, which indicates a feasible and environmentally friendly biostimulation strategy of manipulating nitrogen fixation capacity.

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation

Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.