Biology subjects

Atashgahi, S.

Publications and source records attributed to Atashgahi, S..

6 recordsLinked to original sources

bioRxiv2023

Organohalide respiration by a Desulforhopalus-dominated community

Despite the fact that several potential organohalide-respiring bacteria (OHRB) were discovered in metagenome-assembled genomes (MAGs) in our previous study of marine sediments from Aarhus Bay, delineation of their roles and interactions are yet to be disentangled. Henceforth, obtaining corresponding pure cultures or more defined consortia would be highly instrumental for more detailed eco-physiological studies. To this end, we isolated a colony from an anaerobic slant tube culture inoculated with a stable PCE dehalogenating enrichment. Intriguingly, the derived culture exhibited debromination only, instead of PCE dechlorination, under sulfate-reducing conditions. The culture was capable of conserving energy for growth via debromination of 2,6-dibromophenol (2,6-DBP). Analysis of 16S rRNA gene sequence data extracted from shot gun metagenome sequences revealed that a strain belonging to Desulforhopalus was the predominant member of the consortium at a relative abundance of 29 %. Moreover, five bins (completeness > 85% and contamination < 3%) were assembled and all were identified as potentially new species (average nucleotide identity, ANI < 95%). Two bins from potential OHRB, bin.3 belonging to Desulfoplanes, and bin.4 belonging to Marinifilaceae, were found to encode reductive dehalogenase (RDase) genes, whereas bin.5 was found to contain a gene coding for thiolytic tetrachloro-p-hydroquinone (TPh-) RDase bearing 23.4 % identity to TPh-RDase of Sphingobium chlorophenolicum. The expression of all three RDase genes was strongly-induced after adding 2,6-DBP. Acetylene, a known inhibitor of different redox-active metalloenzymes, was found to inhibit methanogenesis as well as reductive dehalogenation without affecting gene expression, suggesting post-transcriptional inhibition. Phylogenomic analyses revealed the ecological importance of complementary roles of community members, including complete de novo vitamin B12 biosynthesis, which agreed with physiological data. Altogether, the findings presented here provided insight into the mutualism of the consortium and provided leads for synthetic OHR community optimization strategies for in situ bioremediation.

microbiology↗

bioRxiv2023

Genome-resolved transcriptomics reveals novel organohalide-respiring bacteria from Aarhus Bay sediments

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from PCE-respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 high quality bins with over 75 % completeness and less than 5 % contamination. Sixteen bins harbored RDase genes, and were affiliated taxonomically to the class of Bacilli, and phyla of Bacteroidota, Synergistota, and Spirochaetota, that have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically closely related to the genus Vulcanibacillus, contained an unprecedented 97 RDase genes. Of these, 84 RDase genes of bin.26 were transcribed during PCE dechlorination in addition to RDase genes from members of Synergistales (bin.15 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested the RDase genes were likely under the regulation of transcriptional regulators not previously associated with OHR, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to provide evidence towards the diversity, activity and regulation of reductive dehalogenases.

microbiology↗

bioRxiv2020

Biodiversity and niche partitioning in an anaerobic benzene degrading culture

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and free energy source and nitrate as the electron acceptor. We demonstrate that only a few community members are able to degrade benzene, and that most of the others feed on the metabolic left-overs or on the contents of dead cells making up a food web with different trophic levels. As a result of niche partitioning, a high species richness is maintained and the complexity of a natural community is stabilized in a relatively simple environment. This view highlights the importance of species interactions and interdependencies, which drive microbial community structure and function. These mechanisms may well be conserved across ecosystems.

ecology↗

bioRxiv2019

Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. The lack of CF removal in the abiotic control cultures without artificial electron donors indicated that the observed CF removal is a biotic process. Metabolite analysis with 13C labelled CF in the sediment-free enrichment cultures (pH 8.5, salinity 5%) revealed that increasing the vitamin B12 concentration from 0.04 to 4 M enhanced CF removal, reduced DCM formation, and increased 13CO2 production, which is likely a product of CF oxidation. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected by quantitative PCR nor metagenomic analysis. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected in the enrichment cultures. Genome-resolved metagenome analysis indicated that their genomes encode enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis that are known to be involved in co-metabolic CF transformation. ImportanceMore than 90% of the global CF emission to the atmosphere originates from natural sources, including saline environments such as salt lake sediments. However, knowledge about the microbial metabolism of CF in such extreme environments is lacking. Here we showed CF transformation potential in a hypersaline lake that was reported as a natural source of CF production. Application of interdisciplinary approaches of microbial cultivation, stable isotope labelling, and metagenomics aided in defining potential chloroform transformation pathways. This study indicates that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere, and expands our knowledge of halogen cycling in extreme hypersaline environments.

microbiology↗

bioRxiv2019

Exploring groundwater microbial communities for natural attenuation potential of micropollutants

Groundwater is a key water resource, with 45.7% of all drinking water globally being extracted from groundwater. Maintaining good groundwater quality is thus crucial to secure drinking water. Micropollutants, such as pesticides, threaten groundwater quality which can be mitigated by biodegradation. Hence, exploring microbial communities in aquifers used for drinking water production is essential for understanding micropollutants biodegradation capacity. This study aimed at understanding the interaction between groundwater geochemistry, pesticide presence, and microbial communities in aquifers used for drinking water production. Two groundwater monitoring wells located in the northeast of The Netherlands and at 500 m distance from each other were sampled in 2014, 2015, 2016 and 2018. In both wells, water was extracted from five discrete depths ranging from 13 to 54 m and used to analyze geochemical parameters, pesticide concentrations and microbial community dynamics using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (g/L range). Integration of the groundwater chemical and microbial data showed that geochemical parameters and pesticides exerted selective pressure on microbial communities. Furthermore, microbial communities in both wells showed a more similar composition in the deeper part of the aquifer as compared to shallow sections, suggesting vertical differences in hydrological connection. This study provides initial insights into microbial community composition and distribution in groundwater systems in relation to geochemical parameters. This information can contribute for the implementation of bioremediation technologies that guarantee safe drinking water production from clean aquifers. Importance sectionGroundwater is an essential source of drinking water. However, its quality is threathened by the presence of micropollutants. Certain microorganisms are capable of degrading micropollutants. However, groundwater is an unexplored environment, where the biodegradation potential of naturally-present microorganisms is unknown. We thus explore how groundwater microbial ecology in shaped by groundwater composition, namely geochemical parameters and micropollutants. This is a first step towards understanding which microbial communities and environmental conditions support natural attenuation of micropollutants. This study thus provides a first step towards developing in situ bioremediation strategies to remove micropollutants from groundwater used for drinking water production.

microbiology↗

bioRxiv2019

Organohalide-respiring Desulfoluna species isolated from marine environments

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1{top} and D. butyratoxydans MSL71{top} of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third member of this genus from marine intertidal sediment, designed D. spongiiphila strain DBB. All three Desulfoluna strains harbour three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes. Brominated but not chlorinated aromatic compounds were dehalogenated by all three strains. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect OHR. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR (RT-qPCR) revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed differential expression of rdhA1 with 1,4-dibromobenzene, and revealed a possible electron transport chain from lactate dehydrogenases and pyruvate oxidoreductase to RdhA1 via menaquinones and either RdhC, or Fix complex (electron transfer flavoproteins), or Qrc complex (Type-1 cytochrome c3:menaquinone oxidoreductase).

microbiology↗