Shifts In Community Structure Research Articles

Microbiomes of a disease-resistant genotype of Acropora cervicornis are resistant to acute, but not chronic, nutrient enrichment

Chronically high levels of inorganic nutrients have been documented in Florida’s coral reefs and are linked to increased prevalence and severity of coral bleaching and disease. Naturally disease-resistant genotypes of the staghorn coral Acropora cervicornis are rare, and it is unknown whether prolonged exposure to acute or chronic high nutrient levels will reduce the disease tolerance of these genotypes. Recently, the relative abundance of the bacterial genus Aquarickettsia was identified as a significant indicator of disease susceptibility in A. cervicornis, and the abundance of this bacterial species was previously found to increase under chronic and acute nutrient enrichment. We therefore examined the impact of common constituents of nutrient pollution (phosphate, nitrate, and ammonium) on microbial community structure in a disease-resistant genotype with naturally low abundances of Aquarickettsia. We found that although this putative parasite responded positively to nutrient enrichment in a disease-resistant host, relative abundances remained low (< 0.5%). Further, while microbial diversity was not altered significantly after 3 weeks of nutrient enrichment, 6 weeks of enrichment was sufficient to shift microbiome diversity and composition. Coral growth rates were also reduced by 6 weeks of nitrate treatment compared to untreated conditions. Together these data suggest that the microbiomes of disease-resistant A. cervicornis may be initially resistant to shifts in microbial community structure, but succumb to compositional and diversity alterations after more sustained environmental pressure. As the maintenance of disease-resistant genotypes is critical for coral population management and restoration, a complete understanding of how these genotypes respond to environmental stressors is necessary to predict their longevity.

Assessment of a novel continuous cleaning device using metatranscriptomics in diverse hospital environments.

Despite routine implementation of cleaning and disinfection practices in clinical healthcare settings, high-touch environmental surfaces and contaminated equipment often serve as reservoirs for the transmission of pathogens associated with healthcare-associated infections (HAIs). The current study involved the analysis of high-touch surface swabs using a metatranscriptomic sequencing workflow (CSI-Dx™) to assess the efficacy of cleanSURFACES® technology in decreasing microbial burden by limiting re-contamination. This is a non-human single center study conducted in the Emergency Department (ED) and on an inpatient Oncology Ward of Walter Reed National Military Medical Center that have followed hygienic practices during the COVID-19 pandemic environment. Although there was no difference in observed microbial richness (two-tailed Wilcoxon test with Holm correction, P > 0.05), beta diversity findings identified shifts in microbial community structure between surfaces from baseline and post-intervention timepoints (Day 1, Day 7, Day 14, and Day 28). Biomarker and regression analyses identified significant reductions in annotated transcripts for various clinically relevant microorganisms' post-intervention, coagulase-negative staphylococci and Malassezia restricta, at ED and Oncology ward, respectively. Additionally, post-intervention samples predominantly consisted of Proteobacteria and to a lesser extent skin commensals and endogenous environmental microorganisms in both departments. Findings support the value of cleanSURFACES®, when coupled with routine disinfection practices, to effectively impact on the composition of active microbial communities found on high-touch surfaces in two different patient care areas of the hospital (one outpatient and one inpatient) with unique demands and patient-centered practices.

How predictable are mass extinction events?

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to 'predict' the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.

Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures.

Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.

Responses of Nitrous Oxide Emissions and Bacterial Communities to Experimental Freeze-Thaw Cycles in Contrasting Soil Types.

Nitrous oxide (N2O) pulse emissions are detected in soils subjected to freeze-thaw cycles in both laboratory and field experiments. However, the mechanisms underlying this phenomenon are poorly understood. In this study, a laboratory incubation experiment that included freeze-thaw cycles (FTC), freezing (F) and control (CK) treatments was performed on three typical Chinese upland soils, namely, fluvo-aquic soil (FS), black soil (BS) and loess soil (LS). A higher similarity in soil properties and bacterial community structure was discovered between FS and LS than between FS and BS or LS and BS, and the bacterial diversity of FS and LS was higher than that of BS. FTC significantly increased the denitrification potential and the proportion of N2O in the denitrification gas products in FS and LS but decreased the denitrification potential in BS. Accordingly, with the increasing number of freeze-thaw cycles, the bacterial community composition in the FTC treatments in FS and LS diverged from that in CK but changed little in BS. Taxa that responded to FTC or correlated with denitrification potential were identified. Taken together, our results demonstrated that the effects of FTC on N2O emissions are soil-type-dependent and that the shift in the microbial community structure may contribute to the elevated N2O emissions.

The function and community structure of arbuscular mycorrhizal fungi in ecological floating beds used for remediation of Pb contaminated wastewater

Arbuscular mycorrhizal fungi (AMF) have been demonstrated to be ubiquitous in aquatic ecosystems. However, their distributions and ecological functions are rarely studied. To date, a few studies have combined sewage treatment facilities with AMF to improve removal efficiency, but appropriate and highly tolerant AMF strains have not been explored, and the purification mechanisms remain unclear. In this study, three ecological floating-bed (EFB) installations inoculated with different AMF inocula (mine AMF inoculum, commercial AMF inoculum and non-AMF inoculated) were constructed to investigate their removal efficiency for Pb-contaminated wastewater. The AMF community structure shifts in the roots of Canna indica inhabiting EFBs during the three phases (pot culture phase, hydroponic phase and hydroponic phase with Pb stress) were tracked utilizing quantitative real-time polymerase chain reaction and Illumina sequencing techniques. Furthermore, transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to detect the Pb location in mycorrhizal structures. The results showed that AMF could promote host plant growth and enhance the Pb removal efficiency of the EFBs. The higher the AMF abundance, the better the effect of the AMF on Pb purification by EFBs. Both flooding and Pb stress decreased the AMF diversity but did not significantly inhibit the abundance. The three inoculation treatments showed different community compositions with different dominant AMF taxa in different phases, and an uncultured Paraglomus species (Paraglomus sp. LC516188.1) was found to be the most dominant (99.65 %) AMF in the hydroponic phase with Pb stress. The TEM and EDS analysis results showed that the Paraglomus sp. could accumulate Pb in plant roots through their fungal structures (intercellular mycelium, intracellular mycelium, etc.), which alleviated the toxic effect of Pb on plant cells and limited Pb translocation. The new findings provide a theoretical basis for the application of AMF in plant-based bioremediation of wastewater and polluted waterbodies.

Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber

BackgroundPonerine ants are almost exclusively predatory and comprise many of the largest known ant species. Within this clade, the genus Neoponera is among the most conspicuous Neotropical predators. We describe the first fossil member of this lineage: a worker preserved in Miocene-age Dominican amber from Hispaniola.ResultsNeoponera vejestoria sp. nov. demonstrates a clear case of local extinction—there are no known extant Neoponera species in the Greater Antilles. The species is attributable to an extant and well-defined species group in the genus, which suggests the group is older than previously estimated. Through CT scan reconstruction and linear morphometrics, we reconstruct the morphospace of extant and fossil ants to evaluate the history and evolution of predatory taxa in this island system.ConclusionsThe fossil attests to a shift in insular ecological community structure since the Miocene. The largest predatory taxa have undergone extinction on the island, but their extant relatives persist throughout the Neotropics. Neoponera vejestoria sp. nov. is larger than all other predatory ant workers known from Hispaniola, extant or extinct. Our results empirically demonstrate the loss of a functional niche associated with body size, which is a trait long hypothesized to be related to extinction risk.

Acclimation of anaerobic fermentation microbiome with acetate and ethanol for chain elongation and the biochemical response

Medium chain fatty acids (MCFAs) production is a promising method for resource recovery from organic wastes. In this study, the microbial community structure shift along the long-term acclimation experiment and the concomitant effect of H2 level on chain elongation performance was investigated. Chain elongation microbiome could be rapidly acclimated from traditional anaerobic fermentation consortia. Genera Caproiciproducens, Clostridium sensu stricto 12, Rummeliibacillus and Oscillibacter was found to be dominant during the operation. The H2 was accumulated in the headspace by increasing the ethanol input, which inhibited oxidation of caproate and butyrate immediately, while its inhibition effect on chain elongation was delayed. H2 level in the headspace was positively correlated to the MCFAs production related bacteria. However, too much H2 accumulated might be suppressive for MCFAs production in the long term. It might result from the thermodynamic barrier for discarding excess reducing equivalents under high H2 level, which further gave rise to ethanol accumulation in this system.

Bee diversity on urban rooftop food gardens

Green infrastructure on rooftops in urban areas can enhance important ecosystem services. In addition to mitigating water runoff and regulating building temperatures, green roofs can provide food and nesting resources for wildlife. Rooftop gardens can also be utilized to cultivate food crops, giving them the potential to attenuate instances of food insecurity which are commonplace in many urban areas. Given that many crops depend on bee pollination, it is imperative to characterize the rooftop bee community. Therefore, we sampled three urban food roofs near downtown St. Louis, MO during the 2017 and 2018 growing seasons. We found 38 bee species utilizing the rooftop farms. We then compared the rooftop bee communities to those of two nearby ground-level community gardens. The roofs had lower abundances of Bombus species than the ground-level sites while non-native cavity nesters in the genus Megachile were overrepresented. These results indicate that the rooftop bee communities represent a nested subset of the species found at ground level. This has important implications for the management of green roofs for growing crops, as this shift in bee community structure may play a role in determining which crops can be adequately supported with pollination services.

Hydraulic determinants of drought-induced tree mortality and changes in tree abundance between two tropical forests with different water availability

Because of climate change, extreme droughts have become more frequent and caused widespread tree mortality, and thus significant shifts in community structure and function in many forests. Hydraulic failure is a major cause of drought-induced tree mortality. However, its effects on tree dynamics during repeated extreme droughts in tropical forests with different soil water availability are poorly understood. In this study, we surveyed the mortality rate and change in abundance (basal area) for 29 tree species from a humid tropical ravine rainforest (TRF) and an adjacent dry tropical karst forest (TKF) between 2004 and 2015. During this period, two extreme droughts occurred. We measured leaf and stem hydraulic-related traits and analyzed the trait–demography relationships. Our results showed that repeated extreme droughts induced an increase in tree mortality, and thus significantly affected the change of species abundance in the two forest communities. In both forests, the tree species with higher stem embolism resistance were more likely to survive extreme droughts, and increased in basal area during the census period. Moreover, the tree species in the two forests exhibited contrasting hydraulic strategies to deal with extreme drought. The lower mortality rate was associated with larger leaf and stem hydraulic safety margins in the TRF, but with more negative leaf hydraulic safety margin and stronger vulnerability segmentation (larger difference in embolism resistance between leaf and stem) in the TKF. This study expands our understanding of the hydraulic mechanisms to cope with extreme droughts in tropical tree species grown in different substrates under the present and future climatic conditions.

Characterizing the gut microbiome changes with aging in a novel Alzheimer's disease rat model.

Alzheimer's disease (AD) is one of the most devastating diseases currently in the world with no effective treatments. There is increasing evidence that the gut microbiome plays a role in AD. Here we set out to study the age-related changes in the microbiome of the Tgf344-AD rats. We performed 16S ribosomal RNA sequencing on the fecal samples of male rats at 14 and 20 months of age. We found the Tgf344-AD rats to have decreased microbial diversity compared to controls at 14 months of age and this was found to be opposite at 20 months of age. Interestingly, we found a distinctive shift in the microbial community structure of the rats with aging along with changes in the microbiota composition. Some of the observed changes in the Tgf344AD rats were in the genera Bifidobacterium, Ruminococcus, Parasutterella, Lachnoclostridium and Butyricicoccus. Other age-related changes occuring in both the Tgf344-AD and WT control rats were decreases in Enterohaldus, Escherichia Shigella, Rothia and increase in Turicibacter and Clostrium_senso_stricto. Our study has shown that gut microbiota changes occurs in this Alzheimer's disease rat model.

Estimating Effects of Sea Level Rise on Benthic Biodiversity and Ecosystem Functioning in a Large Meso-Tidal Coastal Lagoon.

Estuaries are among the world's most productive ecosystems, but due to their geographic location, they are at the forefront of anthropogenic pressures. Sea level rise (SLR) is one major consequence of climate change that poses a threat to estuaries with extensive intertidal habitats. The ecological implications of intertidal habitat loss have been largely overlooked despite their likely significance. We aimed to address this knowledge gap by investigating how benthic macroinvertebrate communities and their contributions to ecosystem function are likely to respond to SLR. Based on a spatially extensive dataset (119 sites) from a large coastal lagoon, depth, sediment chlorophyll concentrations, mud content, and average current speed were identified as the main drivers of community compositional turnover. Shifts in benthic community structure and associated functional implications were then evaluated using depth as a proxy for SLR. Three main macrofaunal groups representing intertidal, shallow subtidal, and deep subtidal habitats were identified. Functional trait analysis indicated low functional redundancy for a key intertidal suspension-feeding bivalve (Austrovenus stutchburyi) and the lack of a shallow subtidal functional replacement should intertidal habitats become inundated. These findings strongly suggest SLR and the associated environmental changes will alter estuarine macroinvertebrate communities, with implications for future ecosystem function and resilience.

Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan.

To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.

Comparing the Influences of Metformin and Berberine on the Intestinal Microbiota of Rats With Nonalcoholic Steatohepatitis.

High-fat diets induce shifts in the gut microbial community structure in patients or animals with non-alcoholic steatohepatitis (NASH). The objective of this study was to investigate the influence of metformin (MET) and berberine (BER) on the intestinal microbiota of rats with NASH. Forty specific pathogen-free male Sprague-Dawley rats were randomized into 4 groups. Model rats were fed high-fat diets to create NASH models. MET or BER rats were administrated MET or BER, respectively, at the onset of induction of NASH. Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), cholesterol, and triglycerides were examined. Plasma endotoxin levels were measured using the turbidimetric endotoxin assay. The incidence of bacterial translocation describes the passage of bacteria of the gastrointestinal tract through the intestinal mucosa barrier to mesenteric lymph nodes and other organs. Hematoxylin and eosin and oil red O staining were used for histopathological analysis. High throughput 16S rRNA sequencing was carried out for analyzing the composition of intestinal microbiota. High-fat diets caused NASH after 16-week induction. Administration of MET and BER ameliorated NASH by attenuating hepatic steatosis and inflammation and decreasing the plasma levels of endotoxin. MET and BER restored the composition of the intestinal microbiota disrupted by NASH. Both MET and BER altered the abundance of Atopobiaceae, Brevibacterium, Christensenellaceae, Coriobacteriales, Papillibacter, Pygmaiobacter, and Rikenellaceae RC9 in rats with NASH. The screened intestinal microbiota may be responsible for the improvement in fat accumulation and glucose metabolism. MET and BER demonstrated beneficial effects on the intestinal microbiota, which was disturbed in NASH. This finding may explain the functional mechanism of MET and BER in NASH.

Stable colonization of Akkermansia muciniphila educates host intestinal microecology and immunity to battle against inflammatory intestinal diseases

Gut microbial preparations are widely used in treating intestinal diseases but show mixed success. In this study, we found that the therapeutic efficacy of A. muciniphila for dextran sodium sulfate (DSS)-induced colitis as well as intestinal radiation toxicity was ~50%, and mice experiencing a positive prognosis harbored a high frequency of A. muciniphila in the gastrointestinal (GI) tract. Stable GI colonization of A. muciniphila elicited more profound shifts in the gut microbial community structure of hosts. Coexisting with A. muciniphila facilitated proliferation and reprogrammed the gene expression profile of Lactobacillus murinus, a classic probiotic that overtly responded to A. muciniphila addition in a time-dependent manner. Then, a magnetic-drove, mannose-loaded nanophase material was designed and linked to the surface of A. muciniphila. The modified A. muciniphila exhibited enhancements in inflammation targeting and intestinal colonization under an external magnetic field, elevating the positive-response rate and therapeutic efficacy against intestinal diseases. However, the unlinked cocktail containing A. muciniphila and the delivery system only induced negligible improvement of therapeutic efficacy. Importantly, heat-inactivated A. muciniphila lost therapeutic effects on DSS-induced colitis and was even retained in the GI tract for a long time. Further investigations revealed that the modified A. muciniphila was able to drive M2 macrophage polarization by upregulating the protein level of IL-4 at inflammatory loci. Together, our findings demonstrate that stable colonization of live A. muciniphila at lesion sites is essential for its anti-inflammatory function.

Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments.

Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.

Cropping system drives microbial community response to simulated climate change and plant inputs

The soil microbiome’s role in regulating biogeochemical processing is critical to the cycling and storage of soil organic carbon (C). The function of the microbiome under different land management uses has become a focal area of research due to the interest in managing soil C to mitigate climate change. This study investigates the structural and functional response of soil microbiomes from annual monoculture (corn [<i>Zea mays</i> L.]) and perennial diversified (prairie) cropping systems, both under no-till management for bioenergy production. We used a full factorial soil incubation study to understand the influence of temperature and moisture on microbial C decomposition in these soils, with and without addition of cellulose as a model plant residue. Overall, perennial prairie soil supported distinct microbiomes with more diverse prokaryotic and fungal communities compared to annual corn soil. The less diverse corn microbiome was sensitive to the addition of C, resulting in significantly higher respiration compared to prairie, and this increased respiration was amplified under warmer temperatures. In contrast to C loss from the corn soil as carbon dioxide (CO₂), prairie soil had significantly higher extracellular enzyme activities and small increases in microbial biomass, illustrating cropping system-specific tradeoffs between microbial C allocation. Specific community structure shifts occurred with added cellulose, where fast-growing, motile decomposers became more abundant under wet conditions, while a small subset of fungi dominated under dry conditions. These differential responses of fungi and bacteria reflect microbial traits important for accessing substrates like plant residues. These changes in community structure due to moisture and cellulose amendment were not necessarily reflected in community function, as potential enzyme activities of most hydrolases were insensitive to temperature and C amendment on this short time scale. Lower respiration occurred in prairie compared to corn soil in response to increased available C and temperature, indicating a more resistant prairie microbiome that may be beneficial when confronted with climate change. These findings support deploying perennial and diversified systems in place of annual monocultures as bioenergy feedstocks, cover crops, buffer strips, or urban greenspaces as part of a land management strategy and highlight the importance of microbial activity in developing sustainable agroecosystems.

Coupled mixotrophic denitrification and utilization of refractory organics driven by Mn redox circulation for significantly enhanced nitrogen removal

Coupled mixotrophic denitrification and degradation of organics driven by redox transition of Mn for nitrogen removal has attracted much attention. Herein, this study explored the removal performance and mechanisms for nitrogen and refractory organics from secondary effluent in up-flow MnOx biofilter. Results showed that the removal of organics and nitrate was significantly enhanced by the synergistic process of heterotrophic denitrification and Mn(II)-driven autotrophic denitrification (MnAD), which were originated from the facilitation of Mn circulation. But nitrate removal was closely related to the types of carbon source and Mn(II) concentration. Single small molecular carbon source (glucose) performed better than mixed carbon source (humic acid and glucose) in nitrate removal process (74.8% in stage 1–2 vs. 54.1% in stage 3–5). And raising external Mn(II) concentration increased the contribution of MnAD (60.2% in stage 5 vs. 46.5% in stage 3) to nitrate removal. Furthermore, the relationship between Mn/N transformation and microbial community structure shifts revealed that the redox transition between Mn(II) and Mn(IV) promoted the enrichment of denitrogenation bacteria and functional genes, thus contributing to pollutants removal. Our studies expand the knowledge of MnOx-mediated pollutants removal processes and support the potential application of MnOx for removal of residual refractory organics and nitrogen.

Effects of Lake Sediment on Soil Properties, Crop Growth, and the phoD-Harboring Microbial Community

Removal of lake sediment has been shown to be an effective method for lake restoration. High phosphorus (P) content makes it possible for lake sediment to provide fertility for agricultural production. However, little research has focused on the responses of the soil-phosphorus-related microbial community to the sediment-derived fertilizer enriched in phosphorus content. The phoD-harboring gene, important to the global phosphorus cycle, encodes alkaline phosphatase hydrolyzing organic P in soil. Accordingly, a plot experiment was performed to compare the effects of four different fertilization treatments—no-fertilizer control (CK), 50% chemical fertilization with compressed sediment (CS), 50% chemical fertilization with original lake sediment (S), and conventional chemical fertilization treatment (CT)—on the phoD gene community using QPCR and high-throughput sequencing analysis. Relationships among soil physicochemical properties, phoD-harboring microbial community abundance and composition were also evaluated. Results showed that compared to CT, CS significantly increased soil organic matter (SOM) content by 20.29%, and S enhanced the humus content by 20.75% (p &lt; 0.05). There was no significant influence on phoD gene microbial community richness (Chao1 and Sobs indexes) and diversity (Shannon index) between all treatments. The CS treatment significantly altered the phoD community structure and enhanced the Chinese cabbage yield by 40.19% (p &lt; 0.05). Pearson analysis showed that phoD gene abundance (copy number) had significant and negative relationships with SOM, total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), available phosphorus (AP), and the Chao1 index. Redundancy analysis showed that shifts in the phoD community structure were related to soil physicochemical properties (SOM, TN, TP, AN, AP, and humus) rather than soil pH. In conclusion, the compressed sediment can be used in farmland since it optimizes the phoD-harboring microbial community abundance, composition, and structure, and thus significantly increases the Chinese cabbage yield.

Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita.

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.