Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Evaluating groundwater ecosystem dynamics in response to post in-situ remediation of mixed chlorinated volatile organic compounds (CVOCs): An insight into microbial community resilience, adaptability, and metabolic functionality for sustainable remediation and ecosystem restoration

The in-situ remediation of groundwater contaminated with mixed chlorinated volatile organic compounds (CVOCs) has become a significant global research interest. However, limited attention has been given in understanding the effects of these remediation efforts on the groundwater microbial communities, which are vital for maintaining ecosystem health through their involvement in biogeochemical cycles. Hence, this study aimed to provide valuable insights into the impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, employing high-throughput sequencing coupled with functional and physiological assays. The results showed that both bioremediation and chemical remediation methods adversely affected microbial diversity and abundance compared to non-polluted sites. Certain taxa such as Pseudomonas, Acinetobacter, and Vogesella were sensitive to these remediation methods, while Aquabacterium exhibited greater adaptability. Functional annotation unveiled the beneficial impact of bioremediation on the sulfur cycle and specific taxa such as Cellvibrio, Massilia, Algoriphagus, and Flavobacterium which showed a significant positive relationship with dark oxidation of sulfur compounds. In contrast, chemical remediation showed adverse impacts on the nitrogen cycle with a reduced abundance of nitrogen and nitrate respiration along with a reduced utilization of amines (nitrogen rich substrate). The findings of this study offer valuable insights into the potential impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, emphasizing the need for meticulous consideration to ensure the implementation of effective and sustainable remediation strategies that safeguard ecosystem health and function.

Microbial Community Structure of Arsenic-Bearing Groundwater Environment in the Riverbank Filtration Zone

Arsenic (As) contamination of groundwater is a global public health problem. Microorganisms have a great effect on the migration and transformation of arsenic. Studying the effect of microbial community structure and function on arsenic release in the groundwater environment of the riverbank filtration zone has important theoretical and practical significance. In this paper, in-situ monitoring technology and molecular biology technology were used to study the microbial community in the process of river water infiltration in the Shenyang Huangjia water source, China. The results showed that the structure, diversity and abundance of the microbial community in groundwater were closely related to the arsenic content. Proteobacteria was the dominant phylum in groundwater of the study area, and Acinetobacter, Pseudomonas, Sulfuritalea, Sphingomonas and Hydrogenophaga etc. were the main dominant bacterial genera. In addition to reducing and oxidizing arsenic, these functional microorganisms also actively participated in the biogeochemical cycle of elements such as iron, manganese, nitrogen and sulfur. There was a significant correlation between dominant bacteria and environmental factors. Fe/Mn had a significant positive correlation with As, which brought potential danger to the water supply in high iron and manganese areas.

Diversity and arsenic-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high arsenic groundwater of the Hetao Plain, Inner Mongolia

Dissimilatory arsenate reduction from arsenic (As)-bearing minerals into highly mobile arsenite is one of the key mechanisms of As release into groundwater. To detect the microbial diversity and As-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high As groundwater in the Hetao Plain of Inner Mongolia, China, three anaerobic arsenate-reducing bacteria were isolated and arrA and arsC gene-based clone libraries of four in situ groundwater samples were constructed. The strains IMARCUG-11(G-11), IMARCUG-C1(G-C1) and IMARCUG-12(G-12) were phylogenetically belonged to genera Paraclostridium, Citrobacter and Klebsiella, respectively. They could reduce >99% of 1 mM arsenate under anoxic conditions with lactate as a carbon source in 60 h, 72 h and 84 h, respectively. As far as we know, this was the first report of arsenate reduction by genus Paraclostridium. Compared with strain G-11 (arsC) and G-C1 (arsRBC), strain G-12 contained two incomplete ars operons (operon1: arsABC, operon2: arsBC), indicating that these strains might present different strategies to resist As toxicity. Phylogenetic analysis illuminating by the arrA genes showed that in situ arsenate-reducing bacterial communities were diverse and mainly composed of Desulfobacterales (53%, dominated by Geobacter), Betaproteobacteria (12%), and unidentified groups (35%). Based on the arsC gene analysis, the indigenous arsenate-reducing bacterial communities were mainly affiliated with Omnitrophica (88%) and Deltaproteobacteria (11%, dominated by Geobacter and Syntrophobacterales). Results of this study expanded our understanding of indigenous arsenic-reducing bacteria in high As groundwater aquifers.

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling

The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH₄ concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO₄^2--reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater

A pilot-scale biofilter treating real groundwater was developed in this study, which showed that ammonia, iron and manganese were mainly removed at 0.4, 0.4 and 0.8 m of the filter bed, respectively, and the corresponding removal efficiencies were 90.82%, 95.48% and 95.90% in steady phase, respectively. The variation of microbial populations in the biofilter during start-up process was also investigated using high-throughput pyrosequencing (HTP). Results indicated that the main functional microbes for ammonia, iron and manganese removal were Nitrosomonas, Crenothrix and Crenothrix, respectively, which was mainly distributed at 0.8, 0, and 0.8 m of the filter bed with a corresponding abundance of 8.7%, 28.12% and 11.33% in steady phase, respectively. Kinds of other bacteria which may be related to methane, hydrogen sulfide and organic matter removal, were also found. In addition, small part of archaea was also detected, such as Candidatus Nitrososphaera, which plays a role in nitritation.

Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions

Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination. Comprehensive geochemical analyses and 16S rRNA gene amplicon sequencing demonstrated distinct soil taxonomic inventories depending on Sb and As contamination levels. Stochastic gradient boosting indicated that citric acid extractable Sb(V) and As(V) contributed 5% and 15%, respectively, to influencing the community diversity. Random forest predicted that low concentrations of Sb(V) and As(V) could enhance the community diversity but generally, the Sb and As contamination impairs microbial diversity. Co-occurrence network analysis indicated a strong correlation between the indigenous microbial communities and various Sb and As fractions. A number of taxa were identified as core genera due to their elevated abundances and positive correlation with contaminant fractions (total Sb and As concentrations, bioavailable Sb and As extractable fractions, and Sb and As redox species). Shotgun metagenomics indicated that Sb and As biogeochemical redox reactions may exist in contaminated soils. All these observations suggest the potential for bioremediation of Sb- and As-contaminated soils.

Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment

Aquabacterium parvum strain B6 exhibited efficient nitrate-dependent Fe(II) oxidation ability using nitrate as an electron acceptor. A continuous up-flow bioreactor that included an aerobic and an anoxic section was constructed, and strain B6 was added to the bioreactor as inocula to explore the application of microbial nitrate-dependent Fe(II) oxidizing (NDFO) efficiency in wastewater treatment. The maximum NRE (anoxic section) and TNRE of 46.9% and 79.7%, respectively, could be obtained at a C/N ratio of 5.3:1 in the influent with HRT of 17. Meanwhile, the taxonomy composition of the reactor was assessed, as well. The NDFO metabolism of strain B6 could be expected because of its relatively dominant position in the anoxic section, whereas potential heterotrophic nitrification and aerobic denitrification developed into the prevailing status in the aerobic section after 50days of continuous operation.