Changes In Bacterial Community Structure Research Articles

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L)

Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested Bt-chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native Mesorhizobium under field environment. Quantitative variations for nodulation traits among Bt-chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from Bt-chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to Firmicutes and Actinobacteria were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13–14 times lesser than that of parent cv DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non-Bt and Bt-chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of Mesorhizobium with a low relative abundance of 0.27. The impact of Bt-transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.

Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.

Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

BackgroundThe shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing.ResultsOJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3−-N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions.ConclusionSoil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

Maize root and shoot litter quality controls short-term CO<sub>2</sub> and N<sub>2</sub>O emissions and bacterial community structure of arable soil

Abstract. Chemical composition of root and shoot litter controls decomposition and, subsequently, C availability for biological nitrogen transformation processes in soils. While aboveground plant residues have been proven to increase N2O emissions, studies on root litter effects are scarce. This study aimed (1) to evaluate how fresh maize root litter affects N2O emissions compared to fresh maize shoot litter, (2) to assess whether N2O emissions are related to the interaction of C and N mineralization from soil and litter, and (3) to analyze changes in soil microbial community structures related to litter input and N2O emissions. To obtain root and shoot litter, maize plants (Zea mays L.) were cultivated with two N fertilizer levels in a greenhouse and harvested. A two-factorial 22 d laboratory incubation experiment was set up with soil from both N levels (N1, N2) and three litter addition treatments (control, root, root + shoot). We measured CO2 and N2O fluxes, analyzed soil mineral N and water-extractable organic C (WEOC) concentrations, and determined quality parameters of maize litter. Bacterial community structures were analyzed using 16S rRNA gene sequencing. Maize litter quality controlled NO3- and WEOC availability and decomposition-related CO2 emissions. Emissions induced by maize root litter remained low, while high bioavailability of maize shoot litter strongly increased CO2 and N2O emissions when both root and shoot litter were added. We identified a strong positive correlation between cumulative CO2 and N2O emissions, supporting our hypothesis that litter quality affects denitrification by creating plant-litter-associated anaerobic microsites. The interdependency of C and N availability was validated by analyses of regression. Moreover, there was a strong positive interaction between soil NO3- and WEOC concentration resulting in much higher N2O emissions, when both NO3- and WEOC were available. A significant correlation was observed between total CO2 and N2O emissions, the soil bacterial community composition, and the litter level, showing a clear separation of root + shoot samples of all remaining samples. Bacterial diversity decreased with higher N level and higher input of easily available C. Altogether, changes in bacterial community structure reflected degradability of maize litter with easily degradable C from maize shoot litter favoring fast-growing C-cycling and N-reducing bacteria of the phyla Actinobacteria, Chloroflexi, Firmicutes, and Proteobacteria. In conclusion, litter quality is a major driver of N2O and CO2 emissions from crop residues, especially when soil mineral N is limited.

Study on degradation characteristics and bacterial community structure changes of immobilized cells in straw-alginate beads in marine environment

Immobilized bioremediation technology is widely used in treating oil-contaminated seas, but changes of bacterial community during treatment were rarely known. In this study, two diesel-degrading strains were embedded in straw-alginate beads to form immobilized cells. Diesel degradation properties and morphological characteristics of the immobilized cells were obtained by gas chromatography–mass spectrometry (GC–MS) and scanning electron microscope (SEM). Bacterial community structure was observed by high-throughput sequencing. The results indicated that C11~C17 was more degraded by immobilized cells, and straw-alginate beads had appropriate pore structure. Higher bacterial diversity was observed in the bioremediated seawater. Pseudoalteromonas (26.41%), became the most dominant species after oil spills, and Thalassospira was enriched to 25.89% after bioremediation. Concentration of oil degradation related genes was predicted to be higher in the bioremediated seawater. Hence, immobilized cells in straw-alginate beads were suitable for degradation diesel. This study was expected to improve the actual repair effect of oil spills.

Biochar application increased methane emission, soil carbon storage and net ecosystem carbon budget in a 2-year vegetable–rice rotation

The effect of biochar application on the net ecosystem carbon budget (NECB) and the mechanism controlling methane (CH4) emission in paddy soils under vegetable–rice rotations are poorly understood. A 2-year field experiment was conducted with three treatments: control (no fertilizer or biochar application), chemical fertilizer (BC0) and biochar plus chemical fertilizer application (BC1) to analyze greenhouse gas (GHG) fluxes, soil organic carbon (SOC) content, as well as the abundance and community structure of methanogens and methanotrophs in a vegetable–rice rotation. Biochar addition (BC1) did not affect the yield, or the emission of total CH4 or nitrous oxide (N2O) but significantly increased carbon dioxide (CO2) emission as compared to BC0 in the vegetable season. Rice yield in BC1 was 14.1 % higher than in the control but was lower than in BC0 because of lower available nutrients in BC1 than in BC0. During the rice season, cumulative CH4 emission under BC1 was increased by 2.65 times as compared with BC0 (P < 0.01), in association with an increase in methanogenic and decrease in methanotrophic gene abundances. The cumulative CO2 emission was not different between BC0 and BC1 while cumulative and yield-scaled N2O emissions were significantly higher in BC1 than in BC0 in the rice season. However, BC1 increased SOC and NECB, but decreased the ratio of carbon (C) emission to C sequestration, net global warming potential (NGWP) and greenhouse gas emission intensity (NGHGI) as compared to the BC0 and control treatments (P < 0.01). The increase in GHG emissions in the biochar-amended soil was compensated by the increase in soil C storage and C uptake by rice, based on NGWP and NGHGI. The increase in NECB and SOC in the BC1 treatment indicates the benefit of biochar in restoring SOC during the rice season. This study provides insights into the effects of biochar addition on changes in bacterial abundance and community structure which increased CH4 emission in the rice season of a vegetable–paddy rotation.

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure.

An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.

Myriophyllum elatinoides growth and rhizosphere bacterial community structure under different nitrogen concentrations in swine wastewater

In this study, Myriophyllum elatinoides growth under different nitrogen (N) concentrations (2, 250, 300, 350 and 400 mg L−1) and changes in rhizosphere bacterial community structure were investigated. High N (>300 mg L−1) concentrations caused reduction in M. elatinoides biomass. Growth tended to stabilize at 49 days. N concentration in roots were higher than that in stems and leaves under high N conditions. TN and NH4+ removal efficiencies reached 84.0% and 87.2%, respectively, in M. elatinoides surface flow constructed wetlands (SFCWs). Rhizosphere bacterial diversity increased over time. Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes dominated at the phylum level. Genera Turicibacter, Allochromatium, and Methylocystis increased at low N (<300 mg L−1) concentrations, while Pseudomonas increased at high N concentrations over the experimental period. Redundancy analysis showed that pH was strongly correlated with changes in rhizosphere bacterial community structure. These findings helped to insight into N removal mechanism in M. elatinoides.

Change of bacterial community structure in nonylphenols-degrading sediments

Change of bacterial community structure in nonylphenols-degrading sediments

Influence of Diclofenac on Activated Sludge Bacterial Communities in Fed-Batch Reactors.

SUMMARYResearch backgroundThe occurrence and environmental toxicity of pharmaceuticals have recently attracted increasing attention. Diclofenac is a highly consumed non-steroidal anti-inflammatory drug, which is often detected in wastewaters, but investigations of its influence on bacteria are scarce.Experimental approachWe investigated the influence of this pharmaceutical on bacterial community in activated sludge exposed to increasing concentrations of diclofenac in fed-batch reactors over 41 days. Nitrification activity of the activated sludge was measured and changes in bacterial community structure were followed using culture-independent molecular method (terminal restriction fragment length polymorphism, T-RFLP) and by the cultivation approach.Results and conclusionsNitrification activity was not detectably influenced by the addition of diclofenac, while the main change of the bacterial community structure was detected only at the end of incubation (after 41 days) when diclofenac was added to artificial wastewater as the only carbon source. Changes in community composition due to enrichment were observed using cultivation approach. However, taxonomic affiliation of isolates did not match taxons identified by T-RFLP community profiling. Isolates obtained from activated sludge used as inoculum belonged to five genera: Comamonas, Arthrobacter, Acinetobacter, Citrobacter and Aeromonas, known for their potential to degrade aromatic compounds. However, only Pseudomonas species were isolated after the last enrichment step on minimal agar plates with diclofenac added as the sole carbon source.Novelty and scientific contributionOur results suggest that the selected recalcitrant and commonly detected pharmaceutical does not strongly influence the sensitive and important nitrification process of wastewater treatment. Moreover, the isolated strains obtained after enrichment procedure that were able to grow on minimal agar plates with diclofenac added as the only carbon source could serve as potential model bacteria to study bacterial diclofenac degradation.

Transition of the Bacterial Community and Culturable Chitinolytic Bacteria in Chitin-treated Upland Soil: From Streptomyces to Methionine-auxotrophic Lysobacter and Other Genera.

Chitin amendment is an agricultural management strategy for controlling soil-borne plant disease. We previously reported an exponential decrease in chitin added to incubated upland soil. We herein investigated the transition of the bacterial community structure in chitin-degrading soil samples over time and the characteristics of chitinolytic bacteria in order to elucidate changes in the chitinolytic bacterial community structure during chitin degradation. The addition of chitin to soil immediately increased the population of bacteria in the genus Streptomyces, which is the main decomposer of chitin in soil environments. Lysobacter, Pseudoxanthomonas, Cellulosimicrobium, Streptosporangium, and Nonomuraea populations increased over time with decreases in that of Streptomyces. We isolated 104 strains of chitinolytic bacteria, among which six strains were classified as Lysobacter, from chitin-treated soils. These results suggested the involvement of Lysobacter as well as Streptomyces as chitin decomposers in the degradation of chitin added to soil. Lysobacter isolates required yeast extract or casamino acid for significant growth on minimal agar medium supplemented with glucose. Further nutritional analyses demonstrated that the six chitinolytic Lysobacter isolates required methionine (Met) to grow, but not cysteine or homocysteine, indicating Met auxotrophy. Met auxotrophy was also observed in two of the five type strains of Lysobacter spp. tested, and these Met auxotrophs used d-Met as well as l-Met. The addition of Met to incubated upland soil increased the population of Lysobacter. Met may be a factor increasing the population of Lysobacter in chitin-treated upland soil.

Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability.

Rationale: Differences in cystic fibrosis (CF) airway microbiota between periods of clinical stability and exacerbation of respiratory symptoms have been investigated in efforts to better understand microbial triggers of CF exacerbations. Prior studies have often relied on a single sample or a limited number of samples to represent airway microbiota. However, the variability in airway microbiota during periods of clinical stability is not well known.Objectives: To determine the temporal variability of measures of airway microbiota during periods of clinical stability, and to identify factors associated with this variability.Methods: Sputum samples (N = 527), obtained daily from six adults with CF during 10 periods of clinical stability, underwent sequencing of the V4 region of the bacterial 16S ribosomal RNA gene. The variability in airway microbiota among samples within each period of clinical stability was calculated as the average of the Bray-Curtis similarity measures of each sample to every other sample within the same period. Outlier samples were defined as samples outside 1.5 times the interquartile range within a baseline period with respect to the average Bray-Curtis similarity. Total bacterial load was measured with droplet digital polymerase chain reaction.Results: The variation in Bray-Curtis similarity and total bacterial load among samples within the same baseline period was greater than the variation observed in technical replicate control samples. Overall, 6% of samples were identified as outliers. Within baseline periods, changes in bacterial community structure occurred coincident with changes in maintenance antibiotics (P < 0.05, analysis of molecular variance). Within subjects, bacterial community structure changed between baseline periods (P < 0.01, analysis of molecular variance). Sample-to-sample similarity within baseline periods was greater with fewer interval days between sampling.Conclusions: During periods of clinical stability, airway bacterial community structure and bacterial load vary among daily sputum samples from adults with CF. This day-to-day variation has bearing on study design and interpretation of results, particularly in analyses that rely on single samples to represent periods of interest (e.g., clinical stability vs. pulmonary exacerbation). These data also emphasize the importance of accounting for maintenance antibiotic use and granularity of sample collection in studies designed to assess the dynamics of CF airway microbiota relative to changes in clinical state.

Short-term warming shifts microbial nutrient limitation without changing the bacterial community structure in an alpine timberline of the eastern Tibetan Plateau

The forest-alpine ecotone is consideredsusceptible to climate change. Addressing the effects of climate warming on the structure and function of the soil microbial community will provide insights into carbon (C) and nutrient cycling under climate change. A short-term open-top chamber (OTC) experiment was conducted in the alpine timberline of the eastern Tibetan Plateau to test the effects of experimental warming on the soil bacterial community composition, extracellular enzymes, ecoenzymatic stoichiometry and soil physicochemical properties. The results showed that there were no significant changes in the soil bacterial alpha-diversity, composition or community structure in response to soil warming. However, during the early growing season, two carbon-degrading enzymes (β-glucosidase, BG; peroxidase, POD) and microbial carbon limitation decreased with soil warming in the mineral soil layer, which might be a result of an increasing accumulation of soil C. We also observed that C:P enzyme ratios decreased and the relative microbial P limitation increased with soil warming in the organic soil layer. Our db-RDA results demonstrate that both available nutrient pools (dissolved organic carbon and total dissolved nitrogen) and total nutrient concentrations (soil organic carbon and total nitrogen), in addition to soil pH and moisture content, affected soil bacterial communities. These findings suggest that short-term soil warming may change the microbial C and P demand, although bacteria showed temperature adaptability to soil warming.

Manure application increased denitrifying gene abundance in a drip-irrigated cotton field.

Application of inorganic nitrogen (N) fertilizer and manure can increase nitrous oxide (N2O) emissions. We tested the hypothesis that increased N2O flux from soils amended with manure reflects a change in bacterial community structure and, specifically, an increase in the number of denitrifiers. To test this hypothesis, a field experiment was conducted in a drip-irrigated cotton field in an arid region of northwestern China. Treatments included plots that were not amended (Control), and plots amended with urea (Urea), animal manure (Manure) and a 50/50 mix of urea and manure (U+M). Manure was broadcast-incorporated into the soil before seeding while urea was split-applied with drip irrigation (fertigation) over the growing season. The addition treatments did not, as assessed by nextgen sequencing of PCR-amplicons generated from rRNA genes in soil, affect the alpha diversity of bacterial communities but did change the beta diversity. Compared to the Control, the addition of manure (U+M and Manure) significantly increased the abundance of genes associated with nitrate reduction (narG) and denitrfication (nirK and nosZ). Manure addition (U+M and Manure) did not affect the nitrifying enzyme activity (NEA) of soil but resulted in 39–59 times greater denitrifying enzyme activity (DEA). In contrast, urea application had no impact on the abundances of nitrifier and denitrifier genes, DEA and NEA; likely due to a limitation of C availability. DEA was highly correlated (r = 0.70–0.84, P < 0.01) with the abundance of genes narG, nirK and nosZ. An increase in the abundance of these functional genes was further correlated with soil NO3−, dissolved organic carbon, total C, and total N concentrations, and soil C:N ratio. These results demonstrated a positive relationship between the abundances of denitrifying functional genes (narG, nirK and nosZ) and denitrification potential, suggesting that manure application increased N2O emission by increasing denitrification and the population of bacteria that mediated that process.

The responses of bacterial community and N2O emission to nitrogen input in lake sediment: Estrogen as a co-pollutant

Excessive nitrogen (N) input is one of the most important causative factors of lake eutrophication, which has aroused increasing public attention in past decades. Estrogen contamination is also an increasing environmental problem in aquatic systems around the world. Although both substances usually co-exist in aquatic ecosystems, many researches have only investigated the influences of either N or estrogen individually on sediment bacterial community and nitrous oxide (N2O) emission. Knowledge regarding the combined effects of N and estrogen is still very limited. In this study, a 30-day laboratory incubation experiment was performed to examine the impacts of different N sources (ammonium and nitrate) combined with 17β-estradiol (E2) on sediment bacterial community. High-throughput 16S rRNA gene sequencing technique was used and N2O emission was measured. The results revealed that the relative abundances of Proteobacteria and Bacteroidetes were higher in nitrate treatment than ammonium treatment. Compared to N treatments, N and E2 combined treatments showed higher relative abundances of Proteobacteria, Bacteroidetes, and Firmicutes, but lower relative abundances of Chloroflexi, Acidobacteria, and Actinobacteria over entire incubation period. At the genus level, the relative abundances of genera Flavobacterium, Pseudomonas, Arenimonas, Novosphingobium, Massilia, Aquabacterium, and Bacillus were enhanced by N treatments and especially N and E2 combined treatments, compared to sediment without addition of N and E2. However, the relative abundances of Sporacetigenium, Gaiella, Desulfatiglans, Nitrospira, and Haliangium were decreased in N treatments. Apart from the changes in bacterial community structure, N2O emission was also influenced by different treatments. Nitrate exerted a more significant positive effect on N2O emission than ammonium, and the cumulative emission of N2O was highest in nitrate and E2 combined treatment. Very low abundances of ammonia monooxygenase (amoA) gene and hydroxylamine oxidase (hao) gene were observed in sediments compared to other genes involved in N cycles (such as nitrate reductase (narG and napA) genes, nitrite reductase (nirB, nirK, and nrfA) genes, and nitric oxide reductase (norB) gene), implying that denitrification rather than nitrification played an important role in sediments. The abundances of napA, nirK, and norB were higher in N and E2 combined treatments, indicating that E2 might provide a carbon source for denitrifiers. Moreover, decrease in the abundance of nitrous oxide reductase (nosZ) gene during the denitrifying process in N and E2 combined treatment might be an important reason for increases of N2O emission. These results indicated that alterations of the bacterial community structure due to the co-existence of N and E2 could also change the abundances of genes involved in N cycle.

Soil acidification in continuously cropped tobacco alters bacterial community structure and diversity via the accumulation of phenolic acids

Studying the obstacles associated with continuous cropping is necessary for sustainable agricultural production. Phenolic acids play an important role in continuous cropping systems, although their mechanism of action in these systems remains unclear. Using High-performance Liquid Chromatography, we characterized the changes in phenolic acid contents in soils that had been continuously cropped with tobacco for different time periods and evaluated the interactions between soil physicochemical properties, bacterial community structure and diversity, and phenolic acids. Prolonged continuous cropping was associated with a significant increase in the content of phenolic acids and a significant decrease in soil pH and bacterial diversity. A significant negative correlation between pH and phenolic acids content was observed, suggesting that soil acidification potentially leads to the accumulation of phenolic acids. The Mantel test indicated that phenolic acids were positively associated with relative bacterial abundance (R = 0.480, P < 0.01), signifying that the accumulation of phenolic acids is a potential factor leading to changes in bacterial community structure. Continuous cropping lowered the soil pH, which stimulated phenolic acid accumulation and consequently altered the bacterial community structure and diversity, ultimately impacting tobacco plant growth.

Restriction of plant roots in boreal forest organic soils affects the microbial community but does not change the dominance from ectomycorrhizal to saprotrophic fungi.

Boreal forest soils store significant amounts of carbon and are cohabited by saprotrophic and ectomycorrhizal fungi (ECM). The 'Gadgil effect' implies antagonistic interactions between saprotrophic fungi and ECM. Plant photosynthates support the competitive fitness of the ECM, and may also shape the soil bacterial communities. Many 'Gadgil effect' experiments have focused on litter layer (OL) or have litter and root-fragments present, and thus possibly favor the saprotrophs. We compared how the restriction of plant roots and exudates affect soil microbial community structures in organic soil (mixed OF and OH). For this, we established a 3-yr field experiment with 3 different mesh treatments affecting the penetration of plant roots and external fungal hyphae. Exclusion of plant photosynthates induced modest changes in both fungal and bacterial community structures, but not to potential functionality of the microbial community. The microbial community was resilient towards rather short-term disturbances. Contrary to the 'Gadgil effect', mesh treatments restricting the entrance of plant roots and external fungal hyphae did not favor saprotrophs that originally inhabited the soil. Thus, we propose that different substrate preferences (fresh litter vs. fermented or humified soil), rather than antagonism, maintain the spatial separation of saprotrophs and mycorrhizal fungi in boreal forest soils.

Physico-chemical properties and bacterial community structure dynamics during the mesophilic anaerobic digestion of pit latrine faecal sludge

The study characterized the changes in physico-chemical properties and bacterial community structure during mesophilic anaerobic digestion (AD) of pit latrine sludge. The sludge was sampled from six different pits six times at an interval of 40 days. Standard techniques were used to assess the changes in pollution indicators including COD and faecal coliforms. Metagenomic DNA from a composite sample from the six pits’ sludge was then extracted at Days 0, 14 and 35 and directly sequenced followed by analysis of the microbial structure using the Ribosomal Database Project tools. Multivariate analyses were used to identify the main determinants of microbial community structure during the digestion process. AD significantly reduced the levels of pollution indicators (p &lt; 0.05). Total solids, volatile solids and COD were reduced by 17–27%, 52–79%, and 42– 63%, respectively. The indicator pathogenic microorganisms FC and E. coli were reduced by 34–54% and 35–60%, respectively. The reduction in terms of COD and BOD were, however, not sufficient to satisfy the standards for safe disposal into the environment. Proteobacteria were the most dominant bacterial phylum in the undigested sludge (24.1%) and were significantly reduced to 2.5% at the peak of the AD (Day 14) up until Day 35. Firmicutes significantly increased (p &lt; 0.05) from 22.4% to 28.8% at Day 14 before being reduced to 11.6% at Day 35. This study contributes to our understanding of AD of pit latrine faecal sludge through mesophilic AD as a baseline study, and helps to inform future research on mesophilic AD.

Biostimulation of calcite precipitation process by bacterial community in improving cement stabilized rammed earth as sustainable material.

Rammed earth has been enjoying a renaissance as sustainable construction material with cement stabilized rammed earth (CSRE). At the same time, it is important to convert CSRE to be a stronger, durable, and environment-friendly building material. Bacterial application is established to improve cementitious materials; however, bioaugmentation is not widely acceptable by engineering communities. Hence, the present study is an attempt applying biostimulation approach to develop CSRE as sustainable construction material. Results showed that biostimulation improved the compressive strength of CSRE by 29.6% and resulted in 27.7% lower water absorption compared to control. The process leading to biocementation in improving CSRE was characterized by Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscope-energydispersive spectrometer. Further, Illumina MiSeq sequencing was used to investigate changes in bacterial community structures after biostimulation that identified majority of ureolytic bacteria dominated by phylum Firmicutes and genus Sporosarcina playing role in biocementation. The results open a way applying biological principle that will be acceptable to a wide range of civil engineers.

Changes in Cold and Hot Syndrome and Gastrointestinal Bacterial Community Structure in Mice by Intervention with Food of Different Nature.

To reveal the effect of foods with different natures on cold or hot syndrome and gastrointestinal bacterial community structure in mice. Forty-five 6-week-old male ICR Kunming mice of clean grade were divided into 5 groups, 9 per group, including the control (CK), hot nature herbs (HM), Hong Qu glutinous rice wine (RW), tea rice wine (TW), and cold nature herbs (CM) groups. Distilled water or corresponding herbs were administered to mice (0.01 mL/g body weight) in the 5 groups by gastric infusion respectively, once daily for 28 d. Appearance, behavior, and serum biochemical indicators, including 5-hydroxytryptamine (5-HT), thyroid stimulating hormone (TSH), noradrenaline (NE), cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), the hot nature index, as well as the gastrointestinal bacterial community structure were analyzed in all groups after treatment. After supplementation for 28 d, CM and TW mice showed different degrees of cold syndrome, and HM and RW mice showed different degrees of hot syndrome. Compared with the HM and RW mice, the TSH, NE, cAMP levels and hot nature indices in the CM and TW mice were significantly decreased and 5-HT and cGMP levels were significantly increased (P<0.05). There was no obvious change in appearance or behavior in CK mice. Results of clustering analysis showed that the gastrointestinal bacterial community structures were highly similar in TW and CM mice as well as in RW and HM mice, and that they were from the same branch, respectively, when the distance was 0.02. The key microbes associated with cold syndrome were Lachnospiraceae uncultured, Lactococcus, etc., and the key microbes associated with hot syndrome were S24-7 norank, Ruminococcaceae uncultured, etc. CONCLUSION: The interventions with different nature foods could change cold or hot syndrome in mice, leading to changes in gastrointestinal bacterial community structure.