Arsenic and cadmium are inhibitors of cyanobacterial dinitrogenase reductase (nifH1) gene

Cadmium inhibits carbon and nitrogen cycling through soil microbial biomass and reduces soil nitrogen availability

Microbial mediated carbon and nitrogen cycling response to cadmium are often observed in soil; however, a unified framework of this response has not yet been established. By analyzing 1232 observations from 166 publications, we found that cadmium decreased microbial biomass carbon (-16 %) and nitrogen (-21 %), dissolved organic nitrogen (-27 %), nitrification rate (-17 %), microbial respiration rate (-12 %), and β-1,4-glucosidase (-21 %) and urease (-16 %) activities, but increased microbial metabolic quotient (+11 %) and fungal-to-bacterial ratio (+39 %). The cadmium impact was concentration-dependent, becoming more pronounced at higher concentrations. Increasing cadmium concentration reduced soil N mineralization rate and total N content, but increased microbial biomass carbon-to-nitrogen ratio. These results indicate that cadmium reduced carbon and nitrogen assimilation into microbial biomass and limited soil inorganic nitrogen production. Soil bulk density drove soil microbial biomass and nitrogen availability response to cadmium. Lower soil bulk density and higher initial carbon and clay contents and soil pH reduced the negative impact of cadmium on microbial biomass and nitrogen availability, suggesting that anthropogenic activities that enhance soil quality may mitigate the inhibitory effect of cadmium on soil carbon and nitrogen cycling. Our analysis provides critical implications for improving our understanding of the ecological consequences of cadmium on soil carbon and nitrogen cycling.

Comparative analysis of DNA binding and abiotic stress tolerance of Dps All4145 and its homologs in Anabaena PCC 7120

BACKGROUND

DNA-binding proteins under starvation (Dps) are mini-ferritins that sequester iron at the ferroxidase center (FOC) of a hollow protein cage. This study characterizes the novel Dps-All4145. Discrepancies between computational predictions and experimental stress responses were addressed using an integrated computational and experimental approach. Additionally, site-directed mutagenesis was performed to explore the mechanistic link between DNA binding and ferroxidation.

METHODS AND RESULTS

This study involves the molecular characterization of the novel Dps-All4145 and a comparative biochemical and structural analysis of four Dps homologs (Alr3808, All0458, All1173, and All4145) from Anabaena sp. PCC 7120. In-silico and wet lab approaches were employed to assess their biochemical functions, including iron oxidation and DNA protection. The study confirmed that iron oxidation and DNA protection are common attributes of all four Dps homologs. Additionally, all homologs contributed to abiotic stress management. Among them, Alr3808 exhibited the highest efficiency in iron oxidation and DNA protection. Site-directed mutagenesis of Alr3808K49R led to the loss of DNA-binding ability and a 60% reduction in iron oxidation, indicating the crucial role of the N-terminal lysine (K49) residue in these activities.

CONCLUSION

This study provides first-hand insights into the molecular functions of Dps proteins in Anabaena sp. PCC 7120 and highlights the unique significance of K49 in Alr3808 for iron oxidation and DNA binding.

Biochar amendment reduces biological nitrogen fixation and nitrogen use efficiency in cadmium-contaminated paddy fields

Cadmium (Cd) contamination poses a considerable threat to human health through grain enrichment and limits biological nitrogen fixation (BNF) in paddy fields. Biochar has shown great potential for agricultural soil remediation because it inactivates Cd, but uncertainties remain as to how biochar amendments affect BNF and grain N use efficiency in paddies. To elucidate these issues, we investigated the effects of biochar amendment on the structure and function of diazotrophic bacterial communities in different rice growth stages in Cd-contaminated paddy fields, and evaluated the contribution of BNF to grain N use efficiency under biochar amendment. The results showed that biochar amendment significantly increased the abundance of diazotrophic bacteria in the tillering and jointing stages. Furthermore, the community structure of soil diazotrophic bacteria markedly changed with biochar amendment, with a significant reduction in the abundances of Euryarchaeota, Desulfobacterales (Proteobacteria), and Sphingomonadales (Bacteroidetes) in the tillering stage. Changes in the soil carbon/nitrogen (C/N) ratio was the main factor driving diazotrophic microbial community characteristics caused by the release of available C from biochar at the tillering stage, rather than the Cd. Moreover, biochar amendment increased the efficiency of BNF (especially for autotrophic N2 fixation) in the vegetative phase of rice growth. Notably, biochar amendment significantly decreased BNF efficiency during the filling stage and reduced grain N use efficiency. The limited available nutrients in biochar and the toxicity of polycyclic aromatics and phenols in biochar-derived dissolved organic matter were responsible for the varied impacts of biochar on BNF in different rice growth stages. For the first time, we report that biochar amendment in paddy soils reduces Cd toxicity but also inhibits BNF and thereby decreases N use efficiency. Therefore, before applying biochar to inactivate Cd in paddy fields, there should be a trade-off between agricultural production and ecological safety to achieve sustainable agriculture.

Functional and mechanistic insights into the differential effect of the toxicant 'Se(IV)' in the cyanobacterium Anabaena PCC 7120

Selenium, an essential trace element for animals, poses a threat to all forms of life above a threshold concentration. The ubiquitously present cyanobacteria, a major photosynthetic biotic component of aquatic and other ecosystems, are excellent systems to study the effects of environmental toxicants. The molecular changes that led to beneficial or detrimental effects in response to different doses of selenium oxyanion Se(IV) were analyzed in the filamentous cyanobacterium Anabaena PCC 7120. This organism showed no inhibition in growth up to 15 mg/L sodium selenite, but above this dose i.e. 20-100 mg/L of Se(IV), both growth and photosynthesis were substantially inhibited. Along with the increased accumulation of non-protein thiols, a consistent reduction in levels of ROS was observed at 10 mg/mL dose of Se(IV). High dose of Se(IV) (above 20 mg/L) enhanced endogenous reactive oxygen species (ROS)/lipid peroxidation, and decreased photosynthetic capability. Treatment with 100 mg/L Se(IV) downregulated transcription of several photosynthesis pathways-related genes such as those encoding photosystem I and II proteins, phycobilisome rod-core linker protein, phycocyanobilin, phycoerythrocyanin-associated proteins etc. Interestingly, at a dose range of 10-15 mg/L Se(IV), Anabaena showed an increase in PSII photosynthetic yield and electron transport rate (at PSII), suggesting improved photosynthesis. Se was incorporated into the Anabaena cells, and Se-enriched thylakoid membranes showed higher redox conductivity than the thylakoid membranes from untreated cells. Overall, the data supports that modulation of photosynthetic machinery is one of the crucial mechanisms responsible for the dose-dependent contrasting effect of Se(IV) observed in Anabaena.

Elevated level of arsenic negatively influences nifH gene expression of isolated soil bacteria in culture condition as well as soil system

Comprehensive studies on the effect of arsenic (As) on free-living diazotrophs that play a crucial role in soil fertility by nitrogen fixation are still scanty. Here, we isolated three free-living bacteria from rice field with potential nitrogen-fixing ability and investigated the impact of As on their nifH gene expression and extracellular polysaccharide (EPS) production in culture condition and soil system. 16S rRNA sequence analysis showed that the isolated bacteria were affiliated to β-Proteobacteria, γ-Proteobacteria and Firmicutes. As(III) exposure to bacterial isolates followed by RT-qPCR analysis revealed that elevated levels of As reduced the expression of nifH gene in selective bacteria, both in culture medium and soil condition. We also noticed reduced production of EPS under higher concentration of As. All the three bacteria showed high tolerance to As(III), able to oxidize As and exhibited significant plant growth-promoting traits. This investigation indicated that an environment exposed with higher concentration of As might perturbed the activity of free-living diazotrophs in agricultural soil system.

Temporal dynamics of total and free-living nitrogen-fixing bacterial community abundance and structure in soil with and without history of arsenic contamination during a rice growing season

Despite the fact that the nitrogen (N) fixers act as the key regulator of ecosystem process, a detailed study of their abundance, diversity, and dynamics in arsenic (As)-contaminated rice fields is missing so far. DNA extracted from soil followed by 16S rRNA and nifH gene-based real-time qPCR, clone library analysis, and DNA sequencing were used to examine the status of the total and diazotrophic communities in two agricultural fields with and without arsenic contamination history during one rice cultivation season. In general, higher nifH and 16S rRNA gene copy numbers were observed in rice growing soils with lesser As than that with higher As. Elevated levels of 16S rRNA and nifH genes in soil is directly associated with total and nitrogen fixers abundance in the agricultural land without As contamination history through the cultivation period, but the copy number of 16S rRNA gene was decreased, and the nifH gene remained unchanged in the As-contaminated land. Additionally, Canonical Correspondence Analysis (CCA) indicated the possible suppression of nifH gene abundance by soil pH, phosphate, and As content. Increased abundance of total and Acidobacterial lineages in low As-containing soil and the detection of several uncultured groups among nifH gene sequence in higher frequency indicated the presence of novel nifH bearing bacterial groups. Conversely, the abundance of copiotrophic Proteobacterial lineages gradually increased in soil with higher As. Herein, our study demonstrated that the dynamics of free-living nitrogen-fixing bacterial communities were perturbed due to As contamination in agricultural land.

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.