Total Community Research Articles

Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons.

Fungal species participate in vast numbers of processes in the landscape around us. However, their cryptic mycelial growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enables identification and relative quantification of fungal community members across well-replicated experimental settings.Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, i.e., the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon pool to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.

Internal and external microbiota of home-caught Anopheles coluzzii (Diptera: Culicidae) from Côte d'Ivoire, Africa: Mosquitoes are filthy.

Over the past 10 years, studies using high-throughput 16S rRNA gene sequencing have shown that mosquitoes harbor diverse bacterial communities in their digestive system. However, no previous research has examined the total bacteria community inside versus outside of mosquitoes and whether bacteria found on the outside could represent a potential health threat through mechanical transfer. We examined the bacterial community of the external surface and internal body of female Anopheles coluzzii adults collected from homes in Côte d'Ivoire, Africa, by Illumina sequencing of the V3 to V4 region of 16S rRNA gene. Anopheles coluzzii is in the Anopheles gambiae sensu lato (s.l.) species complex and important in the transmission of malaria. The total 16S rRNA reads were assigned to 34 phyla, 73 orders, 325 families, and 700 genera. At the genus level, the most abundant genera inside and outside combined were Bacillus, Staphylococcus, Enterobacter, Corynebacterium, Kocuria, Providencia, and Sphingomonas. Mosquitoes had a greater diversity of bacterial taxa internally compared to the outside. The internal bacterial communities were similar between homes, while the external body samples were significantly different between homes. The bacteria on the external body were associated with plants, human and animal skin, and human and animal infections. Internally, Rickettsia bellii and Rickettsia typhi were found, potentially of importance, since this genus is associated with human diseases. Based on these findings, further research is warranted to assess the potential mechanical transmission of bacteria by mosquitoes moving into homes and the importance of the internal mosquito microbiota in human health.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea.

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 103 CFU·mL-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins.

Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.

Effect of fresh and aged biochar on electrogenic hydrocarbon degradation in soil microbial electrochemical remediation

The remediation of petroleum hydrocarbon-contaminated soil is a global problem. A bioelectrochemical system (BES) is an environmentally friendly technique. In BESs, microbes on the anode play central roles in electricity generation and pollutant degradation. Here, we utilized fresh and aged biochar (marked by FB and AB) as amendments to assess the spatial-temporal hydrocarbon removal, bacterial community shift and functional gene changes in the anode and cathode vicinity. After 78 days, an accumulated charge of 750 C for FB was gained, which was 12% and 98% higher than that of AB and the no-biochar control (CK), respectively. Moreover, the removal of total petroleum hydrocarbons was enhanced in the order of CK (17–26%) < AB (22–28%) < FB (24–29%) in the cathodic area, while in the anodic region, the removal was enhanced in the order CK (22–31%) < FB (24–30%) < AB (28–30%) on days 43–78. Additionally, the top six phyla were Proteobacteria, Desulfobacterota, Firmicutes, Chloroflexi, Actinobacteriota and Bacteroidota, accounting for > 92% of the total bacterial community, with a declining tendency over time. The cathode vicinity favoured Proteobacteria growth, whereas the anode region favoured Desulfobacterota and Firmicutes. Functional genes emphasized petroleum hydrocarbons as the carbon source and relationships with nitrogen, sulfur and iron compounds in soil. This study validated the aptitudes and application effects of fresh and aged biochar in BESs.

The devil is in the details: Variable impacts of season, BMI, sampling site temperature, and presence of insects on the post-mortem microbiome.

Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual's post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa. The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.

Fungal and fungal-like diversity in marine sediments from the maritime Antarctic assessed using DNA metabarcoding

We assessed the fungal and fungal-like sequence diversity present in marine sediments obtained in the vicinity of the South Shetland Islands (Southern Ocean) using DNA metabarcoding through high-throughput sequencing (HTS). A total of 193,436 DNA reads were detected in sediment obtained from three locations: Walker Bay (Livingston Island) at 52 m depth (48,112 reads), Whalers Bay (Deception Island) at 151 m (104,704) and English Strait at 404 m (40,620). The DNA sequence reads were assigned to 133 distinct fungal amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Glomeromycota, Monoblepharomycota, Mucoromycota and Rozellomycota and the fungal-like Straminopila. Thelebolus balaustiformis, Pseudogymnoascus sp., Fungi sp. 1, Ciliophora sp., Agaricomycetes sp. and Chaetoceros sp. were the dominant assigned taxa. Thirty-eight fungal ASVs could only be assigned to higher taxonomic levels, and may represent taxa not currently included in the available databases or represent new taxa and/or new records for Antarctica. The total fungal community displayed high indices of diversity, richness and moderate to low dominance. However, diversity and taxa distribution varied across the three sampling sites. In Walker Bay, unidentified fungi were dominant in the sequence assemblage. Whalers Bay sediment was dominated by Antarctic endemic and cold-adapted taxa. Sediment from English Strait was dominated by Ciliophora sp. and Chaetoceros sp. These fungal assemblages were dominated by saprotrophic, plant and animal pathogenic and symbiotic taxa. The detection of an apparently rich and diverse fungal community in these marine sediments reinforces the need for further studies to characterize their richness, functional ecology and potential biotechnological applications.

Occurrence, Diversity, and Genomes of "Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments.

The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.

Political Trust in Times of Pandemic: A Survey on The Impact of Covid-19 on The Situation of Refugees in The Kurdistan Region of Iraq

The northern region of Iraq (the KRI) hosts the majority of Syrian refugees and IDPs. The KRI hosts more than 98% of registered Syrian refugees in Iraq. In the KRI, like anywhere else, the pandemic has more socio-economic and psychological impact among the refugee population. According to another report published by the ESCWA, the pandemic has resulted in increased stigma, xenophobia and discrimination. According to the same source, the refugees have been constantly accused of contributing to a wider spread of COVID-19, and of having a significant impact on food security, nutrition and access to basic services. This survey has been conducted to investigate the impact of the pandemic and its ramifications on the refugee community in the KRI. It has been conducted solely among the refugees residing inside the camps located in three KRI governorates, Erbil, Duhok and Suleymania, which represent 39% percent of the total refugee community in the KRI. The research aims to assess the socio-political/economic impact of the COVID-19 situation on the community which lives in the camps across the region, and focuses on the situation of the refugee population inside the camps during the pandemic. It examines (i) the challenges this community faces because of the pandemic; (ii) the way the Syrian refugee communities deal and interact with the news of COVID-19; (iii) the economic impact of the pandemic and the levels of self-reliance and revenues of this community; (iv) this community’s interest in and knowledge of the current issues; (v) the degree of satisfaction with the quality of services in the camps, and (vi) general trust in the state’s institutions.

Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model.

Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.

Active and dormant microorganisms on glacier surfaces.

Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell-specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state-changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze-thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in-situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt-regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds.

Warming shifts the biomass distribution of soil microarthropod communities

Climate warming is often more detrimental to large body sized organisms than small body sized organisms. Yet, how such differential effects of warming at organismal levels affect aggregate community properties, such as community biomass, remains little understood. Here, using geothermally warmed sub-Arctic grassland soils, we investigate how total biomass (product of density and individual body mass) of two major groups of soil microarthropods (Collembola and mites), which are composed of both large and small body sized species, shift in warmed soils when warmed by ∼3–∼6 °C. Our results show that total biomass of Collembola significantly decreased in warmed soils predominantly due to a decline in the density of large body sized species. In contrast, total mite biomass showed a unimodal response to warming. As a result, there was a shift towards mite biomass dominated microarthropod communities in warmed soils. Within Collembola, the deep soil living eu-edaphic functional group declined the most in total biomass, whereas the unimodal response in mites was most pronounced in oribatid mites. Our study highlights that warming induced shifts in total community biomass of soil microarthropods are likely due to greater detrimental effects of warming on several large body sized Collembola.

Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands

Climate influences soil microbial composition and function, but the relative importance of a site's historic climate versus its more immediate environmental conditions is unclear. Using quantitative stable isotope probing (qSIP), we characterized actively growing soil microbial communities and soil properties in three California annual grasslands that span a rainfall gradient and have developed on similar parent material. The soils were assayed in the wet winter season, when environmental conditions are most similar across sites. Since growing populations might be expected to be most responsive to contemporary environmental conditions, we hypothesized that the structure of growing microbial communities would be more similar across the gradient than that of total communities (i.e., including non-growing populations). In addition, we hypothesized that population growth rates would be slowest in the driest site, reflecting a legacy effect of low soil moisture on microbial growth. Soils along the rainfall gradient differed in pH, texture, and cation exchange capacity, but not in total C, C:N or dominant minerals. The radiocarbon (14C) age of soil C (reflecting turnover time) increased with mean annual precipitation but soil respiration was uniformly modern, reflecting microbial reliance on recent C inputs across the sites. The structure of both total and growing microbial communities differed across sites. Across major microbial phyla, including the Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Proteobacteria, bacterial growth rates were consistently lower in the site with the lowest mean annual precipitation. Taxa that were growing at the dry site alone grew more slowly than taxa that grew at multiple sites. These results reflect the influence of climate history and point to the role of environmental filtering at the driest site in shaping its slower growing microbial community, possibly reflecting adaptation to repeated exposure to water stress. Lastly, across taxa, the growth rate of a taxon at one site was correlated with its growth rate in the other sites. This growth rate coherence is likely a consequence of genetically determined physiological traits and is consistent with the idea that evolutionary history constrains growth rate.

Microbiome comparison of Dermanyssus gallinae populations from different farm rearing systems and the presence of common endosymbiotic bacteria at developmental stages.

The hematophagous arthropod, Dermanyssus gallinae (Poultry red mite, PRM) can cause remarkable economic losses in the poultry industry across the globe. Although overall composition of endosymbiotic bacteria has been shown in previous studies, how farm habitats influence the microbiome remains unclear. In the present study, we compared the bacterial communities of D. gallinae populations collected from the cage and free-range farms using next-generation sequences targeting the V3-V4 hypervariable region of the 16S rRNA gene. The QIIME2 pipeline was followed in bioinformatic analyses. Proteobacteria represented a great majority of the total bacterial community of D. gallinae from both farming systems. More specifically, Bartonella-like bacteria (40.8%) and Candidatus Cardinium (21.5%) were found to be predominant genera in free-range and cage rearing systems, respectively. However, the microbiome variation based on farming systems was not statistically significant. In addition, the presence of the five common endosymbiotic bacteria (Wolbachia, Cardinium, Rickettsiella, Spiroplasma, and Schineria) was screened in different developmental stages of D. gallinae. Cardinium was detected in all developmental stages of D. gallinae. On the other hand, Wolbachia and Rickettsiella were only found in adults/nymphs, but neither in the eggs nor larvae. To our knowledge, this study provides the first microbiome comparison at genus-level in D. gallinae populations collected from different farm habitats and will contribute to the knowledge of the biology of D. gallinae.

Evidence for Psammotermes allocerus termite nests as refugium for plant pathogenic microbes: a contribution to generation and maintenance of fairy circles in the Namib Desert

Fairy circles are circular, barren structures in dry grasslands and the mechanisms generating and maintaining them are currently under intense discussion. Here, we analysed bacterial and fungal communities in Namib Desert fairy circle soils, in the tapetum lining of termite nests, the gut of the prevailing sand termite Psammotermes allocerus, and also in the neighbouring grass plants. The total and active microbial communities were analysed through amplicon sequencing of both DNA and RNA extracts, respectively, species-specific PCRs, and through cultivation of bacteria and fungi from the various samples. In the sandy soils, the active bacterial communities were substantially different from the total communities, which suggested the fairy circle soils to be highly selective environments in comparison to other drylands or even temperate soils. This appears to be even more true for fungi as amplification of fungal genes from RNA extracts was not possible. However, we observed a large diversity among cultured fungal species in comparison to cultured bacterial species, specifically in tapetum samples. Our results support the hypothesis that Psammotermes allocerus acts as a vector for plant pathogenic fungi and that their nests below the bare patches of fairy circles provide a refugium for the fungal plant pathogens.

Straw Management and Slurry Application Affect the Soil Microbial Community Composition and Its Activity

In low-input farming systems, where plant nutrition strongly depends on either organic matter inputs or nitrogen fixation by legumes, it is crucial to understand the effects of different crop residue management strategies on microbially mediated processes that influence nutrient dynamics. To evaluate different straw management options, we conducted a pot experiment with the following treatments: (1) control with no straw added (CON), (2) applying straw to the soil surface (SRF), simulating no-till, and (3) straw incorporating straw to the top 10 cm (INC), simulating minimum tillage. Another factor was slurry fertilization (with 3.2 t d.m. ha−1 or without). Throughout the experiment, CO2 efflux (µmol/m2/s) was measured regularly over a period of four months. Soil sampling was performed to monitor the abundance of the total bacterial, crenarchaeal and fungal communities, as well as nitrogen cycle microbial guilds and the dynamics of labile N and C fractions in the soils at different depths. Among straw treatments, significantly higher soil respiration was observed in INC and SRF compared to CON. Slurry fertilization increased soil respiration in all straw treatments. In the top 10 cm soil layer, the fungal abundance increased in INC compared to SRF and CON, whereas bacteria and crenarchaea did not respond. This effect was even more pronounced with slurry addition. The slurry also stimulated the abundance of certain N-cycle guilds, with the greatest increase in bacterial amoA-bearing nitrifiers and nirS, nosZI and nozII-bearing denitrifiers, particularly in the uppermost 0–1 cm soil layer. Straw treatment effects on N-cycle microbial guilds were less pronounced, while the coupled effect of straw incorporation and slurry was beneficial mostly for nosZ, again mainly in the top 1 cm soil layer. Compared to straw management, slurry fertilization had more potent effects on the abundance and performance of the investigated microbial communities.

Influence of Not-for-Profit Hospital Ownership Type on Community Benefit and Charity Care.

Non-profit hospitals are expected to provide charity care and other community benefits to adjust their tax exemption status. Using the Medicare Hospital Cost Report, American Hospital Association Annual Survey, and the American Community Survey datasets, we examined if church-affiliated hospitals spent more on charity care and community benefit. For this analysis, we defined five main categories of community benefits were measured: total community benefit; charity care; Medicaid shortfall; unreimbursed other means-tested services; and the total of unreimbursed education and unfunded research.Multiple regression was used to examine the effect of church ownership, controlling for other factors, on the level of community benefit in 2644 general acute care non-profit hospitals. Descriptive analyses and multiple regression were used to show the relationship between the provision of community benefits and church affiliation including Catholic (CH), other church-affiliated hospitals (OCAH), and non-church affiliated hospitals (NCAH). The non-profit hospital on average spent 6.5% of its total expenses on community benefits. NCAH spent 6.09%, CH spent 7.5%, and OCAH spent 9.4%. Non-profits spent 2.8% of their total expenses on charity care, with the highest charity care spending for OCAH (5.2%), followed by CH (3.9%), and NCAH (2.4%). Regression results showed that CH and OCAH, on average, spent 1.08% and 2.16% more on community benefits than NCAHs. In addition, CH and OCAH spent more on other categories of community benefits except for education and research. Church-affiliated hospitals spend more on community benefits and charity care than non-church affiliated nonprofit hospitals.

Rhodotorula glutinis как компонент биопленок навозных стоков

Analysis of manure biofilm effluents revealed an association of Clostridium ssp. (91.09 %), Escherichia coli (6.07), Bacteroides sp. (1.06), Sarcina ventriculi (0.91), Klebsiella sp. (0.14 %), and yeast Rhodotorula glutinis in the amount of 0.11 % of the total number of microorganisms. The pigmented yeast Rhodotorula glutinis has a low biochemical activity and is resistant to pH changes. In a natural environment (pH 7.0 ±0.3), the amount of Rhodotorula glutinis was 0.11% of the total number of micro- organisms (7*104±2.2 CFU/ml), but with a pH shift to 5.5±0.1 (acidification was carried out with 10 % sulfuric acid solution), the amount of yeast increased to 1.01 % (9*105±1.1 CFU/ml). Yeast of this species retains its viability when the temperature rises, so when heated to 70o C (in bioreactor plants when separating manure effluents), the amount of yeast was 0.06 % of the total microbial community (3*102±1.2 CFU/ml). The detection of yeast Rhodotorula glutinis in pig manure drains has not been described in the domestic and foreign literature before, their role requires further research.

Total and active benthic foraminiferal community and their response to heavy metals revealed by high throughput DNA and RNA sequencing in the Zhejiang coastal waters, East China Sea.

Benthic foraminifera, large protists abundant in marine environments, have been widely used as bioindicators of environmental conditions. In this study, high-throughput sequencing based on small subunit rDNA and rRNA amplifications was used to investigate total and active benthic foraminifera community composition and diversity from nineteen and twelve superficial marine sediment samples in the Zhejiang coastal waters, respectively. The results showed that the dominant taxa of total foraminifera changed from Buliminellidae (hyaline) to Saccamminidae (agglutinated) from north to south along the coastal waters of Zhejiang Province. According to our survey, heavy metal contamination was moderate in Zhejiang coastal waters, and the potential ecological risks posed by Cd and Hg were higher. The contamination level of heavy metals at Yueqing Bay was the highest, followed by those at Sanmen Bay and Hangzhou Bay. Cd, Cu and grain size may be key factors affecting the distribution and composition of active foraminiferal communities.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.