Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of AsIII and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

Characteristics of Culturable Microbial Community in Rhizosphere/Non-rhizosphere Soil of Potentilla Fruticosa Population in Alpine Meadow Elevation Gradient

Potentilla fruticosa is a typical shrub of alpine meadows with canopy effects that can greatly influence soil fertility and microbiological parameters. Changes in rhizosphere microorganisms can reflect the response of these plants to environmental changes. This study aimed to examine the rhizosphere and non-rhizosphere of P. fruticosa on the amount of selected microorganisms and main environmental factors at different elevation gradients (3,000, 3,250, 3,500, 3,750, and 4,000 m). The results suggested that bacteria were predominant of the microbial soil community in the rhizosphere and non-rhizosphere, while fungi and actinomycetes represented the minority. With the increase of altitude, the total amount of microbial, bacteria, and actinomycetes in the rhizosphere and non-rhizosphere of P. fruticosa showed a downward trend, and microbial functional groups showed that the “hump shape” changed, but the fungi showed the opposite. Variance inflation factor (VIF) screening environmental factors and path analysis were obtained. In the rhizosphere soil, bacteria were affected by Soil organic carbon (SOC), and soil bulk density (SBD) became the main environmental limiting factor with the increase of altitude. The main environmental limiting factor of actinomycetes changed from SBD to Soil total (ST). In the non-rhizosphere soil, the bacteria and actinomycetes changed from ST to SOC and SBD, respectively. The main environmental limiting factor of the fungi was SOC in the rhizosphere and non-rhizosphere. Soil water content (SWC) was the main environmental determinant factor for all microbial groups, microbial functional groups were related to Soil total nitrogen (STN). Our results help to understand the relationship between nutrient cycling and the ecosystem function of alpine meadow plant soil microorganisms and provide theoretical support for alpine meadow ecosystem restoration, biodiversity protection, and the use of microbial resources.

Microbial contribution to post-fire tundra ecosystem recovery over the 21st century

Tundra ecosystems have experienced an increased frequency of fire in recent decades, and this trend is predicted to continue throughout the 21st Century. Post-fire recovery is underpinned by complex interactions among microbial functional groups that drive nutrient cycling post-fire. Here we use a mechanistic model to demonstrate an acceleration of the nitrogen cycle post-fire driven by changes in niche space and microbial competitive dynamics. We show that over the first 5-years post-fire, fast-growing bacterial heterotrophs colonize regions of the soil previously occupied by slower-growing saprotrophic fungi. The bacterial heterotrophs mineralize organic matter, releasing organic and inorganic nutrients into the soil. This pathway outweighs new sources of nitrogen and facilitates the recovery of plant productivity. We broadly show here that while consideration of distinct microbial metabolisms related to carbon and nutrient cycling remains rare in terrestrial ecosystem models, they are important when considering the rate of ecosystem recovery post-disturbance and the feedback to soil nutrient cycles on centennial timescales.

Examination of hydrogen cross-feeders using a colonic microbiota model

Background Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. Results An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version. Conclusions Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.

Microbial function is related to behavior of an invasive anuran

Invasive species cause negative environmental and economic impacts worldwide. Their management may be improved by clarifying the role of behavior in advancing invasions. Gut microbial communities are known to affect behavior of wild populations, but their impact on behavior underlying invasiveness remains unexplored. Invasive populations of the cane toad (Rhinella marina) in Australia have expanded across the continent and exhibit variation in behavioral traits along their expansion trajectory, making this an ideal system to investigate the relationship between gut microbes and behaviors. We collected wild female toads from six locations in Queensland (n = 30) and Western Australia (n = 30), and conducted simple tests on behavioral traits previously associated with invasion ability. We investigated the relationships between toad gut microbiota, behavioral traits and the presence and intensity of co-introduced lungworms (Rhabdias pseudosphaerocephala) in toad samples from both ends of their Australian range. Based on 16S rRNA sequencing data, we found that microbiota in cane toad colons were dominated by the phyla Bacteroidetes, Proteobacteria, Firmicutes, Verrucomicrobia, and Fusobacteria. We found significant differences in microbiota composition (p-value < 0.001) between regions and in predicted microbial functional groups (p-value = 0.002). The occurrence of lungworms was strongly associated with variation in both microbial composition and microbial functions. However, the behavioral traits were associated with microbial functional variation, but not microbial compositional variation. These results support the “holobiont concept” (investigating the assemblage associated with a host) to fully understand drivers of invasion and highlight the need for experimental manipulations to detect causal relationships between microbiota, parasites and host behavior.

Effect of management (ecological and conventional) on functional groups of soil microorganisms in coffee agroecosystems with different resilience to climate variability, Colombia

The effect of management (ecological and conventional) on functional groups of microorganisms of soil in agroecosystems with different resilience scores reported to climate variability in Anolaima, Colombia was evaluated. Were found clustering associated with management and cellulolytic bacteria and fungi abundances. No differences found in diversity of phosphate solubilizing or nitrogen-fixing microorganisms, related to management. The diversity of microbial functional groups was affected by the climatic condition of sampling season. Management was relevant in relationships between resilience scores to climate variability and cellulolytic microorganisms; in ecological agroecosystems, biodiversity knowledge, agroecological main structure, and the participation of farmers in organizations were important

Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere

ABSTRACT The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.

Density-Based Separation of Microbial Functional Groups in Activated Sludge

Mechanistic understanding of how activated sludge (AS) solids density influences wastewater treatment processing is limited. Because microbial groups often generate and store intracellular inclusions during certain metabolic processes, it is hypothesized that some microorganisms, like polyphosphate-accumulating organisms (PAOs), would have higher biomass densities. The present study developed a density-based separation approach and applied it to suspended growth AS in two full-scale domestic water resource recovery facilities (WRRFs). Incorporating quantitative real-time PCR (qPCR) and fluorescence in situ hybridization (FISH) analyses, the research demonstrated the effectiveness of density-based separation in enriching key microbial functional groups, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and PAOs, by up to 90-fold in target biomass fractions. It was observed that WRRF process functionalities have significant influence on density-based enrichment, such that maximum enrichments were achieved in the sludge fraction denser than 1.036 g/cm3 for the enhanced biological phosphorus removal (EBPR) facility and in the sludge fraction lighter than 1.030 g/cm3 for the non-EBPR facility. Our results provide important information on the relationship between biomass density and enrichment of microbial functional groups in AS, contributing to future designs of enhanced biological treatment processes for improved AS settleability and performance.