Methylmercury production and degradation by soil microbial communities

Author(s):  
Yu-Rong Liu ◽  
Qiaoyun Huang

<p>Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of microbial communities associated with MeHg production and degradation in paddy soils remain unclear. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA+ sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobacter carrying the hgcA gene. Our structure equation modeling suggested a much stronger link between bacterial community composition and %MeHg, compared to the abundance of methylating gene (hgcA) and edaphic properties. More importantly, random forest models suggested a more important role of non-Hg methylators than Hg methylators in predicting variations of soil %MeHg.</p><p>Microbial demethylation was demonstrated by significantly more degradation of MeHg in the unsterilized soils than the sterilized controls, although more degradation was observed in water-saturated soils than the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing These findings provide new insights into microbial communities associated with MeHg accumulation in paddy soils, with important implications in mitigating the net production and bioaccumulation of MeHg in rice worldwide.</p>

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.


2020 ◽  
Vol 110 (5) ◽  
pp. 1049-1055
Author(s):  
Emily W. Lankau ◽  
Dianne Xue ◽  
Rachel Christensen ◽  
Amanda J. Gevens ◽  
Richard A. Lankau

Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.


2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Gongwen Luo ◽  
Tingting Wang ◽  
Kaisong Li ◽  
Ling Li ◽  
Junwei Zhang ◽  
...  

ABSTRACT Climate change is predicted to alter precipitation and drought patterns, which has become a global concern as evidence accumulates that it will affect ecosystem services. Disentangling the ability of soil multifunctionality to withstand this stress (multifunctionality resistance) is a crucial topic for assessing the stability and adaptability of agroecosystems. In this study, we explored the effects of nutrient addition on multifunctionality resistance to drying-wetting cycles and evaluated the importance of microbial functional capacity (characterized by the abundances of genes involved in carbon, nitrogen and phosphorus cycles) for this resistance. The multifunctionality of soils treated with nitrogen (N) and straw showed a higher resistance to drying-wetting cycles than did nonamended soils. Microbial functional capacity displayed a positive linear relationship with multifunctionality resistance. Random forest analysis showed that the abundances of the archeal amoA (associated with nitrification) and nosZ and narG (denitrification) genes were major predictors of multifunctionality resistance in soils without straw addition. In contrast, major predictors of multifunctionality resistance in straw amended soils were the abundances of the GH51 (xylan degradation) and fungcbhIF (cellulose degradation) genes. Structural equation modeling further demonstrated the large direct contribution of carbon (C) and N cycling-related gene abundances to multifunctionality resistance. The modeling further elucidated the positive effects of microbial functional capacity on this resistance, which was mediated potentially by a high soil fungus/bacterium ratio, dissolved organic C content, and low pH. The present work suggests that nutrient management of agroecosystems can buffer negative impacts on ecosystem functioning caused by a climate change-associated increase in drying-wetting cycles via enriching functional capacity of microbial communities. IMPORTANCE Current climate trends indicate an increasing frequency of drying-wetting cycles. Such cycles are severe environmental perturbations and have received an enormous amount of attention. Prediction of ecosystem’s stability and adaptability requires a better mechanistic understanding of the responses of microbially mediated C and nutrient cycling processes to external disturbance. Assessment of this stability and adaptability further need to disentangle the relationships between functional capacity of soil microbial communities and the resistance of multifunctionality. Study of the physiological responses and community reorganization of soil microbes in response to stresses requires large investments of resources that vary with the management history of the system. Our study provides evidence that nutrient managements on agroecosystems can be expected to buffer the impacts of progressive climate change on ecosystem functioning by enhancing the functional capacity of soil microbial communities, which can serve as a basis for field studies.


2020 ◽  
Author(s):  
Jingjie Hao ◽  
Yen Ning Chai ◽  
Raziel A. Ordóñez ◽  
Emily E. Wright ◽  
Sotirios Archontoulis ◽  
...  

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.


2015 ◽  
Vol 81 (10) ◽  
pp. 3405-3418 ◽  
Author(s):  
Nuria Bonilla ◽  
Carmen Vida ◽  
Maira Martínez-Alonso ◽  
Blanca B. Landa ◽  
Nuria Gaju ◽  
...  

ABSTRACTOne of the main avocado diseases in southern Spain is white root rot caused by the fungusRosellinia necatrixPrill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments againstR. necatrixand analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition ofR. necatrixby this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.


2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Alexa-Kate Byers ◽  
Leo Condron ◽  
Tom Donavan ◽  
Maureen O'Callaghan ◽  
Taoho Patuawa ◽  
...  

ABSTRACT Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.


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