Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater

Metagenomic and FT-ICR MS insights into the mechanism for the arsenic biogeochemical cycling in groundwater

Arsenic (As) is a groundwater contaminant of global concern. The degradation of dissolved organic matter (DOM) can provide a reducing environment for As release. However, the interaction of DOM with local microbial communities and how different sources and types of DOM influence the biotransformation of As in aquifers is uncertain. This study used optical spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomics, and structural equation modeling (SEM) to demonstrate the how the biotransformation of As in aquifers is promoted. The results indicated that the DOM in high-As groundwater is dominated by highly unsaturated low-oxygen(O) compounds that are quite humic and stable. Metagenomics analysis indicated Acinetobacter, Pseudoxanthomonas, and Pseudomonas predominate in high-As environments; these genera all contain As detoxification genes and are members of the same phylum (Proteobacteria). SEM analyses indicated the presence of Proteobacteria is positively related to highly unsaturated low-O compounds in the groundwater and conditions that promote arsenite release. The results illustrate how the biogeochemical transformation of As in groundwater systems is affected by DOM from different sources and with different characteristics.

Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov

The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15-33 °C and 0-1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0-100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7-92.4% (<95%), and digital DNA-DNA hybridization (dDDH) values were within the range of 25.4-45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.

Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas

Two facultatively anaerobic, chemoorganoheterotrophic bacterial strains, designated JR1/69-2-13^T and JR1/69-3-13^T, were isolated from nitrate- and radionuclide-contaminated groundwater (Ozyorsk town, South Urals, Russia). Both strains were found to be motile, Gram-stain negative rod-shaped neutrophilic, psychrotolerant bacteria that grow within the temperature range from 5-10 to 33 °C at 0-3 (0-5)% NaCl (w/v). The major cellular fatty acids were identified as C_16:0, C_16:1 ω7c, C_18:1 ω7c and C_17:0 cyclo. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and unidentified aminophospholipids. The genomic G + C content of strains JR1/69-2-13^T and JR1/69-3-13^T was determined to be 57.2 and 57.9%, respectively. The 16S rRNA gene sequences of the strains showed high similarity between each other (98.6%) and to members of the genera Pusillimonas (96.8-98.4%) and Candidimonas (97.1-98.0%). The average nucleotide identity and digital DNA-DNA hybridization (dDDH) values among genomes of the new isolates and Pusillimonas and Candidimonas genomes were below 84.5 and 28.8%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic and chemotaxonomic characterisation, we propose assignment of strains JR1/69-3-13^T (= VKM B-3223^T = KCTC 62615^T) and JR1/69-2-13^T (= VKM B-3222^T = KCTC 62614^T) to a new genus Pollutimonas as the type strains of two new species, Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., respectively. As a result of the taxonomic revision of the genus Pusillimonas, three novel genera, Allopusillimonas, Neopusillimonas, and Mesopusillimonas are also proposed; and Candidimonas bauzanensis is reclassified as Pollutimonas bauzanensis comb. nov. Genome analysis of the new isolates suggested molecular mechanisms of their adaptation to an environment highly polluted with nitrate and radionuclides.

Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N₂ at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no "conventional" nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems.

Current Concentrations of Zn, Cu, and As in Piggery Wastewater Compromise Nutrient Removals in Microalgae–Bacteria Photobioreactors Due to Altered Microbial Communities

Simple Summary

Photobioreactor systems based on consortia of microalgae and bacteria are a promising, efficient and sustainable alternative for treatment of wastewaters with high nitrogen content, such as piggery wastewater. In these biological systems, microorganisms play a key role in wastewater treatment by degradation of organic matter and accumulation of nutrients into the generated biomass. However, these wastewaters often contain high concentrations of zinc, copper and arsenic, which can severely affect the activity and growth of microorganisms, and so, the wastewater treatment performance. This article studies the effect of high concentrations of zinc, copper and arsenic on microbial communities, specifically microalgae and bacteria, in photobioreactors treating piggery wastewater, with the aim of elucidating their impact on wastewater treatment performance. For this purpose, the growth of microalgae and the composition and structure of bacterial communities exposed to these pollutants were studied. The performance of the reactors was also evaluated by determining the removal of nutrients, zinc, copper and arsenic. The results showed that high concentrations of zinc, copper and arsenic in piggery wastewater significantly affect the microbiome of the reactors without recovery after exposure to these contaminants, resulting in poorer performance of the reactors and compromising the environmental and health impact of treated effluents.

Abstract

The treatment of pig manure is a major environmental issue, and photobioreactors containing consortia of microalgae and bacteria have proven to be a promising and sustainable treatment alternative. This work studies the effect of Cu, Zn and As, three toxic elements frequently present in piggery wastewater, on the performance and microbiome of photobioreactors. After dopage with Zn (100 mg/L), Cu (100 mg/L), and As (500 µg/L), the high biomass uptake of Zn (69–81%) and Cu (81–83%) decreased the carbon removal in the photobioreactors, inhibited the growth of Chlorella sp., and affected heterotrophic bacterial populations. The biomass As uptake result was low (19%) and actually promoted microalgae growth. The presence of Cu and As decreased nitrogen removal, reducing the abundance of denitrifying bacterial populations. The results showed that metal(loid)s significantly affected 24 bacterial genera and that they did not recover after exposure. Therefore, this study makes an important contribution on the impact of the presence of metal(loid)s in piggery wastewater that compromises the overall performance of PBRs, and so, the environmental and health impact of treated effluents.

Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments

The study reports diversity in nitrifying microbial enrichments from low (0·5-5‰) and high (18-35‰) saline ecosystems. Microbial community profiling of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) enrichments was analysed by sequencing 16S rRNA and was processed using Mothur pipeline. The α-diversity indices showed the richness of nitrifying bacterial consortia from the high saline environment and were clustering based on the source of the sample. AOB and NOB enrichments from both the environments showed diverse lineages of phyla distributed in both groups with 38 and 34 phyla from low saline and 53 and 40 phyla in high saline sources, respectively. At class level, α- and γ-proteobacteria were found to be more dominant in both the enrichments. AOBs and NOBs in enrichments from low saline environments were dominated by Nitrosomonadaceae, Gallionellaceae (Nitrotoga sp.) and Ectothiorhodospiraceae and Nitrospira, respectively. Though Chromatiaceae were present in both AOB and NOB enrichments, Nitrosoglobus and Nitrosococcus dominated the AOBs while NOBs were dominated by uncultured genera, whereas Rhizobiales were found in both the enrichments. AOBs and NOBs in enrichments from high saline environments were dominated by Nitrospira-like AOBs, Nitrosomonas and Nitrosococcus genera, whereas ammonia-oxidizing archaea (AOA) group included Nitrosopumilus and Nitrososphaera genera comprising and Nitrospirae, respectively. The majority of the genera obtained in both the salinities were found to be either uncultured or unclassified groups. Results of the study suggest that the AOB and NOB consortia have unique and diverse microbes in each of the enrichments, capable of functioning in aquaculture systems practised at different salinities (0-60 ppt).

Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami

Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.