Impact of Two Water Management Systems on Arsenic Speciation and Microbial Populations in Rice Rhizosphere

Arsenic (As) is a problem with rice production systems throughout the world as high As concentrations are reported in rice grains originating from several parts of the world. This characteristic is mainly due to the flooded conditions utilized in rice culture. We hypothesized that the soluble As concentrations in the rice rhizosphere can be decreased by growing rice more aerobically through intermittent flooding. Intermittent water management practices might also change microbial populations in the rice rhizosphere that might potentially impact As chemistry and bioavailability. Two field-scale experiments were conducted over two years to study the impact of intermittent and continuous flooding on As speciation and microbial populations in the rice rhizosphere. As levels and speciation in the rhizosphere soil, root-plaque and pore-water were determined using a high performance liquid chromatography-inductively coupled plasmamass spectroscopy (HPLC-ICP-MS). The microbial populations were assessed from the rhizosphere soil and root-plaque samples using quantitative polymerase chain reaction (qPCR) and 16S rRNA sequencing. Pore-water and root-plaque total-As concentrations significantly decreased in the intermittent compared to the continuous flood plots. Inorganic arsenite (iAsIII) was predominant in pore-water and inorganic arsenate (iAsV) in root-plaque and soil. Rootplaque sequestered significantly higher levels of As (almost tenfold higher) than the adjacent rhizosphere soil. Grain As concentrations also decreased by 35 to 45 percent in the intermittent compared to the continuously flooded plots. Organic As species, monomethyl and dimethyl arsenate were detected in the rhizosphere with relative increases and decreases among the treatments. Bacteria were the predominant group (91 to 94 percent and 48 to 78 percent of total community in root-plaque and rhizosphere soils, respectively). Archaea were also a major component of rhizosphere soil with their populations being higher under continuous flooding. The relative abundance of iron-reducing bacteria was around 3 to 6 percent of the total community in root-plaque and around 6 to 6 percent in soil, with significantly lower abundance in the intermittent compared to the continuously flooded plots. Results of these studies demonstrated that intermittent flooding could be a potential management option to reduce grain As in rice cultivated on fields with moderate to high As concentrations

Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

This work conducted by ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory. The submitted manuscript has been authored by a contractor of the U.S. Government under contract DE-AC05-00OR22725. Accordingly, the U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes.Conceived and designed the experiments: ACS JJM MP TJP SDB AVP DAE. Performed the experiments: ACS JJM ZKY. Analyzed the data: ACS JJM TY JDVN JZ DAE. Contributed reagents/materials/analysis tools: DAE TCH APA. Wrote the paper: ACS JJM DAE.Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher Cr(VI) may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.Yeshttp://www.plosone.org/static/editorial#pee

Characterization of an In-Situ Soil Organic Carbon (SOC) via a Smart-Electrochemical Sensing Approach

Soil is a vital component of the ecosystem that drives the holistic homeostasis of the environment. Directly, soil quality and health by means of sufficient levels of soil nutrients are required for sustainable agricultural practices for ideal crop yield. Among these groups of nutrients, soil carbon is a factor which has a dominating effect on greenhouse carbon phenomena and thereby the climate change rate and its influence on the planet. It influences the fertility of soil and other conditions like enriched nutrient cycling and water retention that forms the basis for modern ‘regenerative agriculture’. Implementation of soil sensors would be fundamentally beneficial to characterize the soil parameters in a local as well as global environmental impact standpoint, and electrochemistry as a transduction mode is very apt due to its feasibility and ease of applicability. Organic Matter present in soil (SOM) changes the electroanalytical behavior of moieties present that are carbon-derived. Hence, an electrochemical-based ‘bottom-up’ approach is evaluated in this study to track soil organic carbon (SOC). As part of this setup, soil as a solid-phase electrolyte as in a standard electrochemical cell and electrode probes functionalized with correlated ionic species on top of the metalized electrodes are utilized. The surficial interface is biased using a square pulsed charge, thereby studying the effect of the polar current as a function of the SOC profile. The sensor formulation composite used is such that materials have higher capacity to interact with organic carbon pools in soil. The proposed sensor platform is then compared against the standard combustion method for SOC analysis and its merit is evaluated as a potential in situ, on-demand electrochemical soil analysis platform

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation

The meals from many oilseed crops have potential for biofumigation due to their release of biocidal compounds such as isothiocyanates (ITCs). Various ITCs are known to inhibit numerous pathogens; however, much less is known about how the soil microbial community responds to the different types of ITCs released from oilseed meals (SMs). To simulate applying ITC-releasing SMs to soil, we amended soil with 1% flax SM (contains no biocidal chemicals) along with four types of ITCs (allyl, butyl, phenyl, and benzyl ITC) in order to determine their effects on soil fungal and bacterial communities in a replicated microcosm study. Microbial communities were analyzed based on the ITS region for fungi and 16S rRNA gene for bacteria using qPCR and tag-pyrosequencing with 454 GS FLX titanium technology. A dramatic decrease in fungal populations (~85% reduction) was observed after allyl ITC addition. Fungal community compositions also shifted following ITC amendments (e.g., Humicola increased in allyl and Mortierella in butyl ITC amendments). Bacterial populations were less impacted by ITCs, although there was atransient increase in the proportion of Firmicutes, related to bacteria know to be antagonistic to plant pathogens, following amendment with allyl ITC. Our results indicate that the type of ITC released from SMs can result in differential impacts on soil microorganisms. This information will aid selection and breeding of plants for biofumigation-based control of soil-borne pathogens while minimizing the impacts on non-target microorganisms

Response of soil microbial Communities, inorganic and organic soil carbon pools in arid saline soils to alternative land use practices

Soil organic and inorganic carbon (SOC & SIC) and microbial community structure are key indicators of soil quality and productivity in arid-saline soils. Salinity stress and diminishing availability of freshwater (FW) for irrigation are major constraints for productivity and improving soil quality indicators. Using treated wastewater (TW) and implementing climate-smart cropping systems are promising alternatives to replace freshwater usage in intensive cropping systems, however, impacts on the microbial community and net-carbon sequestration potential are not clearly understood. This field study was conducted in an arid saline-soil to investigate soil microbial community structure and soil carbon contents under a combination of treatments comparing bioenergy sorghum (So) and switchgrass (Sg), two irrigation water sources (FW & TW), and gypsum amendment (GA), to a native-soil control. After three years of implementing these treatments, soil samples were collected and analyzed for total carbon (TC), SOC, SIC, microbial biomass-carbon (MBC) and microbial community structure. Results showed that TW increased microbial diversity and shifted the community structure towards copiotroph-dominated prokaryotes. Several predominant and responsive taxa were associated with divergent trends of SOC, SIC and salinity parameters. Both SOC and SIC pools were sensitive to treatments and demonstrated divergent trends, as contents of TC and SOC were higher in TW-treatments, but of SIC were significantly lower in several So_TW treatments. Treatment TW_So_GA assembled a distinctive microbial community structure, accumulated the highest content of SOC (7.66 g kg−1) but recorded the lowest content of SIC (6.63 g kg−1). The lowest content of SOC was observed in native soil (4.58 g kg−1) but contained the highest SIC (8.15 g kg−1). The study results revealed the agronomic systems with higher potential for increasing TC and SOC content in arid-saline soils. Surface soil SIC was responsive to agronomic management, and several treatments produced disparate impacts on SOC and SIC stocks, which warrant for considering TC as the key indicator for assessing carbon sequestration in arid lands

Impact of Indian Mustard (Brassica juncea) and Flax (Linum usitatissimum) Seed Meal Applications on Soil Carbon, Nitrogen, and Microbial Dynamics

There is a critical need to investigate how land application of dedicated biofuel oilseed meals affects soil ecosystems. In this study, mustard (Brassica juncea) and flax (Linum usitatissimum) seed meals and sorghum-sudangrass (Sorghum bicolor) were added to soil at levels of 0, 1, 2.5, and 5% (w/w). Both the type of amendment and application rate affected soil organic C, total C & N, and C & N mineralization. Mustard meal amendment initially inhibited C mineralization as compared to flax, but >50% of mustard and flax organic C was mineralized within 51 d. Nitrogen mineralization was similar for flax and mustard, except for the 2.5% rate for which a lower proportion of mustard N was converted to nitrate. The mustard meal greatly impacted microbial community composition, appearing to select for specific fungal populations. The potential varying impacts of different oilseed meals on soil ecosystems should be considered when developing recommendations for land application

Responses of Soil Phosphorus Fractions to Land-Use Change in Colombian Amazon

Intensive land-use change, the overgrazing of pastures, and the poor soil management in the Amazon region induce significant soil chemical degradation, causing alterations in the soil phosphorus (P) dynamics. Here, we studied the changes in P fractions and availability throughout the soil profile along a chronosequence composed of four study areas representing the typical land-use transition from forest to pasture for extensive cattle ranching in the Colombian Amazon region: (i) Forest—Deforested—Pasture 4 years old and Pasture established >25 years after deforestation. Soil samples collected at 0–10, 10–20, 20–30, and 30–40 cm depth were used for the sequential fractionation of P, determination of acid phosphatase activity and soil organic carbon (C) content, and calculation of C:organic P (Po) ratio and P stocks. Our results showed that the land-use change caused a decrease of 31.1% in the fractions of labile inorganic P, with the mineralization of organic P by phosphatase enzyme playing an essential role in the P availability. Although according to the C:Po ratio of the deeper layer the P seems to be sufficient to satisfy the plant needs of all the land uses assessed, the exploitation of soil nutrients in pastures reduced by 6.1% the moderately and non-labile P stock. Given the role of cattle ranching in the economy of tropical countries, it is imperative to adopt strategies of soil P management to improve P-use efficiency, avoiding the degradation of grazing land resources while ensuring the long-term sustainability of rangeland livestock and decrease further deforestation of the Amazon rainforest

Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley (Hordeum vulgare L.)

Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost

Mercury Methylation by Novel Microorganisms from New Environments

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (<i>hgcAB</i>) was linked to Hg methylation in two bacteria. Here we test if the presence of <i>hgcAB</i> orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although <i>hgcAB</i> orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding <i>hgcAB</i>, we confirmed that possessing <i>hgcAB</i> predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative <i>Firmicutes.</i> Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities