Major Bacterial Community Research Articles

Responses of Methane Emission and Bacterial Community to Fertilizer Reduction Plus Organic Materials over the Course of an 85-Day Leaching Experiment

Methane produced from paddy fields has a negative impact on global climate change. However, the role of soil bacterial community composition in mediating methane (CH4) emission from waterlogged paddy soil using the column experiment is poorly known. In the present study, various fertilization treatments were adopted to investigate the effects of fertilizer reduction combined with organic materials (CK: control; CF: conventional fertilization; RF: 20% fertilizer reduction; RFWS: RF plus wheat straw amendment; RFRS: RF plus rapeseed shell amendment; RFAS: RF plus astragalus smicus amendment) on CH4 emission and soil bacterial community during an 85-day leaching experiment. We hypothesized that the fertilizer reduction plus the organic materials could enrich the bacterial communities and increase CH4 emission. The average CH4 flux varied from 0.03 μg m−2 h−1 to 76.19 μg m−2 h−1 among all treatments in the nine sampling times, which may account for the experimental conditions such as air temperature, moisture, and anthropogenic factors. In addition, high-throughput sequencing was utilized to investigate the alteration of the soil bacterial community structure. It was revealed that the diversity and composition of the bacterial community in the topsoil amended with organic materials underwent significant shifts after the 85-day leaching experiment. Proteobacteria was identified as the dominant phylum of the soil bacteria, with an average proportion of 35.2%. For Firmicutes, the proportion of RFRS (11%) was higher than that in the CK (8%), RF (8%), RFWS (7%), RFAS (6%), and CF (5%) treatments. Additionally, Gammaproteobacteria and Alphaproteobateria were supposed to be the major class bacterial communities, with average proportions of 12.8% and 12.2%, respectively. For the RFWS treatment, the contribution of Alphaproteobateria was the highest among all the bacterial relative abundance. According to the correlation heatmap analysis, the top ten bacterial communities were positively related to soil microbial biomass carbon (MBC) and ammonia nitrogen (NH4+-N) (p < 0.01). The findings also indicated that the RFRS treatment was the favorable management to alleviate CH4 emission during an 85-day leaching experiment or possibly in paddy production. Collectively, these results predict that the impacts of different treatments on CH4 production are strongly driven by soil microbial communities and soil properties, with soil bacteria being more prone to the crop residue degradation stage and more sensitive to soil properties. The discoveries presented in this study will be useful for assessing the efficacy and mechanisms of organic material amendments on CH4 emissions in paddy soil.

Evaluating Bacillus flexus as bioremediators for ammonia removal in shrimp culture water and wastewater and characterizing microbial communities in shrimp pond sludge.

The accumulation of nitrogen compounds in shrimp farming water and effluent presents a major challenge. Ammonia is a form of nitrogen that limits shrimp growth due to its potential toxicity and effects on shrimp health and water quality. This study is aimed at identifying promising bioremediators from shrimp pond sludge to mitigate ammonia levels in both culture water and wastewater and at determining major bacterial communities in sludge using metagenomic analysis. A sludge sample was collected from a shrimp pond in Selangor, Malaysia, to isolate potential ammonia-removing bacteria. Out of 64 isolated strains, Bacillus flexus SS2 showed the highest growth in synthetic basal media (SBM) containing ammonium sulfate at a concentration of 70 mg/L as the sole nitrogen source. The strain was then incubated in SBM with varying pH levels and showed optimal growth at pH 6.5-7. After 24 h of incubation, B. flexus SS2 reduced the ammonia concentration from an initial concentration of 5 to 0.01 mg/L, indicating a 99.61% reduction rate, which was highest in SBM at pH 7. Moreover, the strain showed ammonia removal ability at concentrations ranging from 5 to 70 mg/L. Metagenomic analysis revealed that Proteobacteria was the most abundant phylum in the sludge, followed by Cyanobacteria, Actinobacteria, Chloraflexi, Firmicutes, and Campilobacterota. Bacillus flexus SS2 belongs to the Bacillota phylum and has the potential to serve as a bioremediator for removing ammonia from shrimp culture water and wastewater.

Influence of Elution Characteristics of Steelmaking Slags on Major Bacterial Communities in Biofilms

Steelmaking slags are prospective base materials for seaweed beds, resulting from a continuous process of biofouling, starting from biofilm formation and leading to growing algae. While focusing on biofilm formation, we investigated specific features of steelmaking slags when utilized as a base for seaweed beds by comparing the bacterial communities in marine biofilms between steelmaking slags and artificially produced ones. Genomic DNA was extracted from the biofilms collected on days 3 and 7, and partial 16S rRNA libraries were generated and sequenced by second-generation next-generation sequencing. The read sequences were analyzed using QIIME 2™, then heatmaps and non-metric multidimensional scaling based on the Bray–Curtis dissimilarity index in the R program. Rhodobacteraceae and Flavobacteriaceae were the most dominant family members in all samples on both days 3 and 7. However, Mariprofundus, comprising iron-oxidative bacteria, was predominantly detected in the samples of steelmaking slags on day 7. This suggested that the growth of Mariprofundus was dependent on Fe(II) ion concentration and that steelmaking slags eluted Fe(II) ions more easily than artificial slags. In contrast, Sulfurovaceae, sulfur-oxidizing bacteria, were dominantly present in all samples on day 3, but decreased by day 7, regardless of the sulfur content. It was supposed that engine oil-derived sulfur compounds strongly influenced Sulfurovaceae growth, whereas slag-derived sulfur compounds did not. Heatmap analysis indicated that the submersion period significantly influenced the bacterial communities, regardless of the differences in the main slag content ratios. Summarizing these results, the elution characteristics of steelmaking slags have the potential to influence the formation of marine biofilms, and this formation is significantly influenced by environmental conditions.

Postharvest Preservation of Flammulina velutipes with Isoamyl Isothiocyanate

Flammulina velutipes was treated with 10, 50, and 250 μL L−1 isoamyl isothiocyanate (IAITC), and effects on quality preservation were assessed. IAITC displayed positive effects during the storage of F. velutipes: (i) maintained tissue integrity, reduced weight loss rates; (ii) reduced browning degree by inhibiting the activities of browning-related enzymes; (iii) enhanced activities of two antioxidant enzymes (superoxide dismutase and catalase) and increased ascorbic acid content; (iv) ameliorated microbial spoilage by inhibiting bacterial growth, especially Serratia, a major bacterial community on the surface of F. velutipes; (v) enhanced chitin content and thereby maintained structural integrity; and (vi) maintained levels of Asp, Glu, linoleic acid, and polyunsaturated fatty acids. In conclusion, IAITC reduced catalase activity and total phenolic content in F. velutipes during storage. The most suitable concentration of IAITC in the preservation of F. velutipes was 50 µL L−1.

Comparative analysis of vaginal microbiota sampling using menstrual cups and high vaginal swabs in pregnant women living with HIV-1 infection.

Menstrual cups (MCs) are increasingly used to collect cervicovaginal secretions to characterise vaginal mucosal immunology, in conjunction with high vaginal swabs (HVS) for metataxonomics, particularly in HIV transmission studies. We hypothesised that both methods of collecting bacterial biomass are equivalent for 16S rRNA gene sequencing. Cervicovaginal fluid (CVF) samples from 16 pregnant women with HIV-1 (PWWH) were included to represent the major vaginal bacterial community state types (CST I-V). Women underwent sampling during the second trimester by liquid amies HVS followed by a MC (Soft disc™) and samples were stored at -80°C. Bacterial cell pellets obtained from swab elution and MC (500 µL, 1 in 10 dilution) were resuspended in 120 µL PBS for DNA extraction. Bacterial 16S rRNA gene sequencing was performed using V1-V2 primers and were analysed using MOTHUR. Paired total DNA, bacterial load, amplicon read counts, diversity matrices and bacterial taxa were compared by sampling method using MicrobiomeAnalyst, SPSS and R. The total DNA eluted from one aliquot of diluted CVF from an MC was similar to that of a HVS (993ng and 609ng, p=0.18); the mean bacterial loads were also comparable for both methods (MC: 8.0 log10 16S rRNA gene copies versus HVS: 7.9 log10 16S rRNA gene copies, p=0.27). The mean number of sequence reads generated from MC samples was lower than from HVS (MC: 12730; HVS:14830, p=0.05). The α-diversity metrices were similar for both techniques; MC Species Observed: 41 (range 12-96) versus HVS: 47 (range 16-96), p=0.15; MC Inverse Simpson Index: 1.98 (range 1.0-4.0) versus HVS: 0.48 (range 1.0-4.4), p=0.22). The three most abundant species observed were: Lactobacillus iners, Lactobacillus crispatus and Gardnerella vaginalis. Hierarchical clustering of relative abundance data showed that samples obtained using different techniques in an individual clustered in the same CST group. These data demonstrate that despite sampling slightly different areas of the lower genital tract, there was no difference in bacterial load or composition between methods. Both are suitable for characterisation of vaginal microbiota in PWWH. The MC offers advantages, including a higher volume of sample available for DNA extraction and complimentary assays.

Diversity and predicted functional roles of cultivable bacteria in vermicompost: bioprospecting for potential inoculum.

Vermicompost (VC) harbours diverse microbes, including plant growth-promoting microorganisms (PGPM) that are beneficial for sustainable crop production. Hence, this study aimed to analyse bacterial diversity of VC samples as a first high-throughput screening step towards subsequent targeted isolation of potential bacterial inoculum candidates. To achieve this, bacterial communities in VC collected from five production farms were enriched in nutrient-rich media before high-throughput sequence (HTS) analysis of the partial 16S rRNA gene. HTS analysis revealed 572 amplicon sequence variants (ASVs) in all enriched VC samples. Firmicutes, Proteobacteria, Planctomycetes and Bacteroidetes were the most dominant phyla, while Lysinibacillus, Escherichia-Shigella, Bacillus, Pseudomonas, Clostridium sensu stricto 1, Morganella, Vibrio and Aeromonas were the predominant genera across the enriched VC. The presence of Clostridium sensu stricto 1, Escherichia-Shigella and Vibrio genera, which are potentially pathogenic species, suggests the need to improve vermicomposting efficiency and safety. Predicted functional profiling of the bacterial communities using PICRUSt2 showed abundance profiles of nitrogenases, phosphatases and sulfatases. In addition, the potential to produce siderophore, indole acetic acids (IAA) and phytohormone regulator 1-aminocyclopropane-1-carboxylate (ACC) were predicted. Lysinibacillus, Bacillus, Paenibacillus and Pseudomonas were major bacterial communities with potential plant growth-promoting traits and could serve as resources in bacterial inoculum production. The findings in this study provide insight into the community composition, abundance and the potential functional capability of cultivable bacterial species of enriched VC. This study also points to VC as a suitable source of potentially beneficial bacterial candidates for inoculum production.

Calcium Propionate Supplementation Has Minor Effects on Major Ruminal Bacterial Community Composition of Early Lactation Dairy Cows.

Calcium propionate is one kind of good source for preventing and treating hypocalcemia and ketosis for dairy cows in early lactation. However, little is known about the effects of different feeding levels of calcium propionate on the ruminal bacterial community of early lactation dairy cows. This study aimed to explore the effects of different calcium propionate feeding levels on the ruminal fermentation and bacterial community composition of early lactation dairy cows. Twenty-four multiparous cows were randomly allocated into control (CON), low calcium propionate (LCaP), medium calcium propionate (MCaP), and high calcium propionate (HCaP) groups with six cows per group after calving. The CON group cows were fed the normal total mixed ration (TMR), and the cows of the LCaP, MCaP, and HCaP groups were fed TMR supplemented with 200, 350, and 500 g/day calcium propionate for 35 days after calving, respectively. The rumen fermentation parameters were measured every week, and the ruminal bacterial community composition of the last week was analyzed by 16S rRNA gene sequencing. Under the same diet, the rumen pH showed no difference among the four groups, but the content of microbial crude protein (MCP) and ammonia nitrogen quadratically decreased and linearly increased with calcium propionate supplementation, respectively. The feeding of calcium propionate linearly increased the concentrations of total volatile fatty acid (VFA), acetate, propionate, butyrate, iso-valerate, and valerate in the rumen. In all the treatment groups, Bacteroidetes, Firmicutes, and Proteobacteria were the dominant phyla, and Prevotella_1 and Succiniclasticum were the dominant genera in the rumen. Compared with the CON group, the addition of calcium propionate to the early lactation dairy cows quadratically improved the alpha diversity index of Chao1 estimator and observed species, but had little effect on the relative abundance of the major bacterial at phyla and genera level. These results suggested different levels of calcium propionate supplementation improved the rumen fermentation and the ruminal bacterial diversity but had little impact on the major ruminal bacterial community composition of dairy cows in early lactation.

Deep‐sea wooden shipwrecks influence sediment microbiome diversity

AbstractHistoric shipwrecks function as habitats for benthic organisms by providing food, refuge, and structure. They also form islands of biodiversity on the seabed, shaping microbial ecology and ecosystem processes. This study examined two wooden deep‐sea shipwrecks at 525 and 1800 m water depth and probed their influence on sediment microbiomes and geochemistry. Microbiomes were investigated with 16S rRNA gene amplicon sequencing along 60 m transects extending in four directions from the hulls of the shipwrecks. Distance from shipwrecks and sediment depth both shaped microbiome structure. Archaeal alpha diversity was significantly and positively correlated with proximity to the deeper shipwreck while bacterial diversity was not to either. Archaeal community structure differed at both sites; the deeper site had a higher proportion of Bathyarchaeia and Lokiarchaeia proximate to shipwreck compared to the shallow location. Major bacterial communities were consistent at both sites, however, at the deeper site had higher abundance of Bacteroidetes, Chloroflexi, Desulfofarculales, and Desulfobacteriales. Core microbiome and differential abundance analyses revealed unique taxa nearest the shipwrecks compared to the surrounding seabed including organoheterotrophs, and cellulolytic and sulfur cycling taxa. Sediment carbon content influenced microbiome structure near the shipwrecks (5–10 m). We show that shipwrecks have a distinct sediment microbiome and form unique habitat patches on seabed, resembling those surrounding organic falls. The shipwreck influence was more pronounced at the deeper site, further from terrestrial influences signaling shipwrecks may be a significant source of organic matter in far‐shore oligotrophic settings.

Community scale in-situ rapid biological reduction and resource recovery of food waste

In this study, a community-scale in-situ rapid biological reduction (IRBR) system was applied to achieve the rapid disposal and resource recovery of food waste (FW). A total of 5263 kg FW was processed in the 35 days of stably operation, during which 84.37% total mass reduction and 43.30% volatile solid removal were achieved, and the odor had been effectively controlled. Microbial sequencing results showed that aerobic and facultative thermophilic bacteria were major bacterial community, and vigorous metabolism of both carbohydrate and amino acid were maintained during the IRBR process. The final products have the potential to be recycled as organic fertilizers or bio-solid fuel to realize resource recovery. The results of economic analysis showed that the IRBR system had lower FW disposal costs due to the high automation. These results suggested that the IRBR system was an environmentally friendly, economical and practical method for the FW rapid treatment.

Microflora and umami alterations of different packaging material preserved mushroom (Flammulina filiformis) during cold storage

In order to clarify the effect of nanocomposite-based packaging (NP) on umami and microflora characteristics of F. filiformis during cold storage, the contents of umami amino acids and 5′-nucleotides, equivalent umami concentration (EUC), and microflora succession were investigated. Results showed that NP could delay the degradation of umami components and inhibit bacterial growth in F. filiformis. At the initial stage, the dominant bacteria were Lactobacillus, Thermus and Acinetobacter. After 15 days of storage, the bacteria count in NP reached 7.63 lg cfu/g, which was significantly (P < 0.05) lower than that in control, and the major bacterial communities of packaged F. filiformis were Ewingella, Serratia and Pseudomonas. Moreover, the correlation analysis showed that Lactobacillus, Brevibacillus and Okibacterium were negatively correlated with AMP and IMP 5-nucleotides. Present work suggested that NP could enhance the umami flavor formation and improve the microbial community structure of F. filiformis, resulting in a better commercial quality. The results provided theoretical basis for large-scale applications of NP.

Sinonasal and gastrointestinal bacterial composition and abundance are stable after 1 week of once-daily oral antibiotic treatment for chronic rhinosinusitis.

Despite the widespread prescription of antibiotics for the treatment of chronic rhinosinusitis (CRS), their efficacy remains uncertain. Limited penetration of systemic antibiotics into the sinonasal mucosa has been reported previously by this group. This study aimed to investigate the short-term effects of antibiotics on the sinus and gut microbiota as well as any relationships these had with drug distribution. Thirty subjects undergoing functional endoscopic sinus surgery for CRS were randomized to one of three groups: (1) doxycycline (100mg daily for 7 days); (2) roxithromycin (300mg daily for 7 days); and (3) control (no antibiotics given). Sinonasal and stool samples collected before and after treatment were analyzed using 16S ribosomal RNA (rRNA) gene-targeted amplicon sequencing and Droplet Digital polymerase chain reaction (PCR) for bacterial community composition and the quantification of bacterial DNA, respectively. There were no significant major bacterial community shifts or changes to bacterial diversity and load following the treatment period in all patient groups. Non-significant trend reductions were observed in gut microbial diversity with antibiotics. For the roxithromycin group, sinonasal bacterial diversity was negatively correlated with serum drug levels and reduced overall compared to controls (p<0.05). The relative abundance of Staphylococcus ASV129 in sinonasal samples reduced with increasing mucus doxycycline levels (p=0.01). Antibiotic prescription for CRS should be further investigated because of preliminary evidence of poor sinonasal drug penetration, unproven efficacy, and the potential impact of dysbiosis in the sinuses and off-target sites. Further studies should consider distinguishing the presence of DNA from viable and nonviable bacteria.

Influence of biochar and biochar-based fertilizer on yield, quality of tea and microbial community in an acid tea orchard soil

Biochar combined with chemical fertilizer have been proven to be effective in improving soil fertility and crop yield. However, the effects of biochar-based fertilizer on yield, quality of tea and microbial community composition in tea orchard soil are unclear. To address this, four different treatments including CK (no fertilizer), B (biochar), F (chemical fertilizer), BF (biochar-based fertilizer) were performed in a tea orchard to explore the effects of different fertilizations on tea growth and the soil bacterial and fungal community. After one growing season, the BF increased the yield, 100-sproutweight and sprout density of tea by 39.2%, 26.6% and 10.7%, respectively, compared to CK. Amino acid content of F and BF, caffeine content of B, F and BF and the water extracts in BF were increased than those of CK. Soil bacterial and fungal diversity indices (chao1 and observed species) were generally higher under B than BF and F treatment. Cluster analysis revealed that bacterial and fungal community structures under BF treatment differed from those under CK, B and F treatment. The relative abundance of 10 key bacterial genera and 13 fungal genera were increased under BF treatment, including some plant beneficial microbes such as bacterial genera Rhodanobacter, Mizugakiibacter, Pedobacter, Sphingomonas and Devosia as well as fungal genera Rhodosporidiobolus, Chloridium, Amylocorticium, Clavulina, Inocybe and Mycofalcella. These genera were significantly positive correlated to yield and quality of tea. Redundancy analysis revealed that pH, total nitrogen and available potassium were the major properties shaping soil bacterial community, and dissolved organic carbon, exchangeable Ca, pH and total nitrogen were for fungal community. These results indicated that biochar-based fertilizer altered soil microbial community and enhanced some plant growth-promoting microbes, which were associated with the improvements of yield and quality of tea plants. Thus, the combination of biochar and chemical fertilizer is feasible for the improvements of tea growth and low nutrients acidic tea orchard soil.

Environmental and Anthropogenic Factors Shape Major Bacterial Community Types Across the Complex Mountain Landscape of Switzerland.

Mountain areas harbor large climatic and geographic gradients and form numerous habitats that promote high overall biodiversity. Compared to macroorganisms, knowledge about drivers of biodiversity and distribution of soil bacteria in mountain regions is still scarce but a prerequisite for conservation of bacterial functions in soils. An important question is, whether soil bacterial communities with similar structures share environmental preferences. Using metabarcoding of the 16S rRNA gene marker, we assessed soil bacterial communities at 255 sites of a regular grid covering the mountainous landscape of Switzerland, which is characterized by close location of biogeographic regions that harbor different land-use types. Distribution of bacterial communities was mainly shaped by environmental selection, as revealed by 47.9% variance explained by environmental factors, with pH (29%) being most important. Little additional variance was explained by biogeographic regions (2.8%) and land-use types (3.3%). Cluster analysis of bacterial community structures revealed six bacterial community types (BCTs), which were associated to several biogeographic regions and land-use types but overall differed mainly in their preference for soil pH. BCT I and II occurred at neutral pH, showed distinct preferences for biogeographic regions mainly differing in elevation and nutrient availability. BCT III and IV differed only in their preferred soil pH. BCT VI occurred in most acidic soils (pH 3.6) and almost exclusively at forest sites. BCT V occurred in soils with a mean pH of 4 and differed from BCT VI in preference for lower values of organic C, total nitrogen and their ratio. Indicator species and bipartite network analyses revealed 3,998 OTUs associating to different levels of environmental factors and BCTs. Taxonomic classification revealed opposing associations of taxa deriving from the same phyla. The results revealed that pH, land-use type, biogeographic region, and nutrient availability were the main factors shaping bacterial communities across Switzerland. Indicator species and bipartite network analyses revealed environmental preferences of bacterial taxa. Combining information of environmental factors and BCTs yielded increased resolution of the factors shaping soil bacterial communities and provided an improved biodiversity framework. OTUs exclusively associated to BCTs provide a novel resource to identify unassessed environmental drivers.

Effect of the Organic Loading Rates Increase on Process Stability and Microbial Community Composition during the Anaerobic Digestion of Fresh Vinegar Residue

Anaerobic digestion (AD) was employed to utilize fresh vinegar residue (FVR) in this study. The performance and microbial community structure at increasing organic loading rates (OLRs) were evaluated. The results showed that the mono-fermentation of FVR was unstable at high OLRs due to the high acidity and the high cellulose content of the raw material. The optimum OLR was 2.0 g VS/(L·d), with the maximum average methane yield at 216 mL /g VS. High OLRs (2.5 g VS/(L·d)) led to the irreversible inhibition of AD process, although digester ceased feeding during the recovering stage. The diversity of microbial community decreased at high OLRs. The relative abundance of major bacterial community at different OLRs also varied. The syntrophic volatile fatty acids (VFAs) oxidizing bacteria declined while the acid-producing bacteria became dominant. The close correlation between the AD process stability and the microbial community structure suggested that maintaining a rich and diverse microbial community was essential for the practical application of AD on vinegar residue (VR) utilization.

Reducing food waste in residential complexes using a pilot-scale on-site system

A pilot-scale on-site system combining biological treatment and a drying stage was applied to achieve mass reduction of food waste (FW) at an urban residential complex. The effectiveness of biodegrading the organic portion of FW via microorganisms existing in FW improved by 38.80% by controlling rates of FW loading and air-flow. In one stage of the on-site biological treatment, the major bacterial community was identified to be mesophilic and facultative; Lactobacillus was the most dominant genus, accounting for 78.1% of bacterial community. Total mass reduction of FW approached 90.15% by increasing removal of both moisture and the organic portion of FW. In addition, the solids and liquids of the final by-products have the potential to be recycled into resources such as fertilizer, a bio-solid refuse fuel or external carbon sources for wastewater treatment plants. The proposed decentralized system offers practical and environmental approaches for FW management in residential complexes.

Bacterial community shifts in decomposing cowpats and the subsequent impacts on fecal source indicators for water quality monitoring

Abstract The intensification of dairy farming on the agricultural landscape in New Zealand has raised concerns about pollution sources from dairy fecal runoff into waterways. An important step for mitigation of pollution is the identification of the sources of fecal contamination. An amplicon-based metagenomic assay of the bacterial community mobilised into runoff from decomposing cowpats revealed shifts in the community composition over five and a half months of on-field decomposition. Mobilised fractions from the cowpats showed major bacterial community shifts from the anaerobic bacteria (Clostridiales and Bacteroidales) that dominate the cow rumen and fresh cowpat, to the bacterial Orders of the Actinomycetales, Sphingobacteriales and Flavobacteriales. These bacterial community shifts were in conjunction with summertime conditions of low rainfall and high sunshine hours coupled with reduced water availability. The impacts of these bacterial shifts is discussed in terms of their effects on the indicators used for water quality monitoring: the fecal indicator bacterium, Escherichia coli, and fecal source tracking (FST) markers (host-associated quantitative polymerase chain reaction (qPCR) markers and fecal steroids). The hypothesis that these bacterial community shifts would impact on the steroid ratios used as FST signatures was disproved. The fecal steroids were, therefore, reliable indicators of fecal sources from cowpats, which had been decomposing for up to five and a half months post-deposition. Consistent with the noted bacterial community changes, there were, however, concentration decreases in the bacterial groups targeted by the faecal source qPCR markers, and the E. coli mobilised from decomposing cowpats.

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.

Diversity of sediment bacterial communities in the South Eastern Arabian Sea

The bacterial community structure in the surface sediments of the South Eastern Arabian Sea (SEAS) was assessed using high-throughput Illumina based sequencing. An attempt was also made to evaluate the role of environmental variables on the distribution of the bacterial community. A total of 53 phyla, 111 classes, 155 orders, 179 families, and 215 genera were detected in the study area. There was no significant difference in the major bacterial communities between nearshore and offshore stations whereas the relative abundance of the majority of OTUs showed station/depth wise variation. Proteobacteria was the dominant phylum observed in all the stations, which ranged from 50.3% to 59.9% of the total sequences retrieved. Other abundant phyla observed were Chloroflexi (7.4% of total sequences), Actinobacteria (6.4%), Acidobacteria (5.5%), Nitrospirae (2.7%), Gemmatimonadetes (2.4%), Bacteroidetes (1.5%), candidate phylum “Latescibacteria” (1.4%), and Spirochaetes (1.1%). All the remaining phyla were observed in lower numbers, comprised of <1% of the total sequences. Within the Proteobacteria 63.8% of sequences were Deltaproteobacteria, 21.8% were Gammaproteobacteria and 1.6% were Alphaproteobacteria. The dominant genera observed within the phylum Proteobacteria were Photobacterium, Desulfococcus, Acinetobacter, Pseudomonas, Marinobacter, Nitrospina, and Desulfosarcina. The dominant genera observed under the phylum Chloroflexi were Dehalococcoides, Anaerolinea, Caldilinea, and Thermogemmatispora. Among the environmental variables, total nitrogen and total sulphur were showed influence on the OTUs distribution in the study area. The dominant phyla in the SEAS such as Proteobacteria, Chloroflexi and Nitrospirae were also significantly influenced by these environmental variables.

Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.

Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.

Age-dependent association of gut bacteria with coronary atherosclerosis: Tampere Sudden Death Study.

BackgroundThe gut microbiome is thought to remain stable into old age. Gut bacteria and their translocation may play a role in the development of coronary heart disease (CHD) by modulating cholesterol levels and immune responses, as well as by producing toxic metabolites and bacterial endotoxins. The association of changes in the gut microbiome with the severity of coronary atherosclerosis and the ability of gut bacteria themselves to translocate into coronary plaques has not been studied.Materials and methodsAs a part of the Tampere Sudden Death Study, we measured age-dependent changes in the relative ratios of major intestinal bacterial communities (Bacteroides species [spp.], the Clostridium leptum group, the Clostridium coccoides group, Bifidobacterium spp., Enterobactericeae, Lactobacillus spp.) and Streptococcus spp. in both feces and coronary plaques of the same male autopsy cases (n = 67, age range 44–95) using real-time quantitative PCR (qPCR). The area of coronary atherosclerotic lesions were measured by computer-assisted morphometry. Fecal bacterial DNA measurements from healthy volunteers served as a control for gut bacterial analyses of autopsy cases. The relative amount of bacterial DNA in a sample was determined with the comparative Cq method.ResultsThe relative ratios of fecal Lactobacillus spp., Bifidobacterium spp., the Clostridium coccoides group, and Bacteroides spp. did not differ between controls and autopsy cases and showed no age-dependence. In contrast, the ratios of the Clostridium leptum group, Enterobactericeae, and Streptococcus spp. increased with age. Elevated relative ratios of fecal Enterobactericeae associated with a larger coronary plaque fibrotic area (p = 0.001), and the Clostridium leptum group with a larger calcification area (p = 0.015). Intestinal bacterial DNA could be amplified in 67.6% of the coronary plaques, the most common being Streptococcus spp. (41.0%), followed by Enterobactericeae (12.1%), Clostridium leptum (2.4%), and Lactobacillus spp. (2.4%). The percentages of Streptococcus spp. DNA decreased, and those of Enterobactericeae increased in coronary plaques along with age.ConclusionsDNA of the Clostridium leptum group and pathogenic Enterobactericeae increase in the gut microbiome with age and can be detected in the same individual’s coronary plaques along with pathogenic Streptococcus spp., associating with more severe coronary atherosclerosis.