Microbial Functional Diversity Research Articles

Modified Lipid Extraction Methods for Deep Subsurface Shale.

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery.

Does functional soil microbial diversity contribute to explain within-site plant β-diversity in an alpine grassland and adehesameadow in Spain?

SummaryQuestions Once that the effects of hydrological and chemical soil properties have been accounted for, does soil microbial diversity contribute to explain change in plant community structure (i.e. within-site beta-diversity)? If so, at which spatial scale does microbial diversity operate? Location: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the Urbion Peaks, Soria, central-northern Spain (alpine grassland). Methods The abundance of vascular plant species, soil gram-negative microbial functional types and soil chemical properties (pH, available phosphorus, and extractable cations) were sampled at both sites, for which hydrological models were available. Redundancy analysis (RDA) was used to partition variation in plant community structure into hydrological, chemical and microbial components. Spatial filters, arranged in scalograms, were used to test for the spatial scales at which plant community structure change. Results In the case of the dehesa the diversity of soil gram-negative microbes, weakly driven by soil pH, contributed to a small extent (adj-R2 = 2%) and at a relative medium spatial scale to explain change in plant community structure. The abundance of a few dehesa species, both annual (Trifolium dubium, Vulpia bromoides) and perennial (Poa bulbosa, Festuca ampla), was associated with either increasing or decreasing soil microbial diversity. In the alpine meadow the contribution was negligible. Conclusions Microbial diversity can drive community structure, though in the hierarchy of environmental factors structuring communities it appears to rank lower than other soil factors. Still, microbial diversity appears to promote or restrain individual plant species. This paper aims to encourage future studies to use more comprehensive and insightful techniques to assess microbial diversity and to combine this with statistical approaches such as the one used here. This article is protected by copyright. All rights reserved.

Changes of soil microbial communities during decomposition of straw residues under different land uses

Monitoring soil microbial communities can lead to better understanding of the transformation processes of organic carbon in soil. The present study investigated the changes of soil microbial communities during straw decomposition in three fields, i.e., cropland, peach orchard and vineyard. Straw decomposition was monitored for 360 d using a mesh-bag method. Soil microbial metabolic activity and functional diversity were measured using the Biolog-Eco system. In all three fields, dried straws with a smaller size decomposed faster than their fresh counterparts that had a larger size. Dried corn straw decomposed slower than dried soybean straw in the early and middle stages, while the reverse trend was found in the late stage. The cropland showed the highest increase in microbial metabolic activity during the straw decomposition, whereas the peach orchard showed the lowest. There was no significant change in the species dominance or evenness of soil microbial communities during the straw decomposition. However, the species richness fluctuated significantly, with the peach orchard showing the highest richness and the cropland the lowest. With different carbon sources, the peach orchard utilised carbon the most, followed by the cropland and the vineyard. In all three fields, carbon was utilized in following decreasing order: saccharides>amino acids>polymers>polyamines>carboxylic acids>aromatic compounds. In terms of carbon-source utilization, soil microbial communities in the peach orchard were less stable than those in the cropland. The metabolic activity and species dominance of soil microbial communities were negatively correlated with the straw residual percentage. Refractory components were primarily accumulated in the late stages, thus slowing down the straw decomposition. The results showed that dried and crushed corn straw was better for application in long-term fields. The diversity of soil microbial communities was more stable in cropland than in orchards during the straw decomposition.

Crop rhizospheric microbial community structure and functional diversity as affected by maize and potato intercropping

ABSTRACTField trials were conducted to evaluate the effects of different cropping patterns (maize monocropping, maize and potato intercropping, potato monocropping) on microbial abundance, community structure, and microbial functional diversity using plate culture and Biolog technique. Results showed that compared with monocropping, intercropping increased the abundance of soil bacteria, fungi, and actinomyces in rhizosphere surrounding maize and potato. The average well color development (AWCD) and Shannon index (H) were higher in intercropping soil than that found in monocropping soil. The ability of rhizospheric soil microorganisms in utilizing six types of carbon sources had definite differences, and the most dominant community structure was the carbohydrates metabolic groups. Principal component analysis demonstrated that intercropping changed significantly soil microbial community functional diversity depending mainly on carbohydrates and carboxylic acids. Our findings suggested that maize–potato intercropping has positive effects on the improvement of soil microbial abundances, activity, and functional diversity.

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau

The structure and function of soil microbial communities have been widely used as indicators of soil quality and fertility. The effect of biochar application on carbon sequestration has been studied, but the effect on soil microbial functional diversity has received little attention. We evaluated effects of biochar application on the functional diversities of microbes in a loam soil. The effects of biochar on microbial activities and related processes in the 0–10 and 10–20cm soil layers were determined in a two-year experiment in maize field on the Loess Plateau in China. Low-pyrolysis biochar produced from maize straw was applied into soils at rates of 0 (BC0), 10 (BC10) and 30 (BC30)tha−1. Chemical analysis indicated that the biochar did not change the pH, significantly increased the amounts of organic carbon and nitrogen, and decreased the amount of mineral nitrogen and the microbial quotient. The biochar significantly decreased average well colour development (AWCD) values in Biolog EcoPlates™ for both layers, particularly for the rate of 10tha−1. Biochar addition significantly decreased substrate richness (S) except for BC30 in the 0–10cm layer. Effects of biochar on the Shannon-Wiener index (H) and Simpson's dominance (D) were not significant, except for a significant increase in evenness index (E) in BC10 in the 10–20cm layer. A principal component analysis clearly differentiated the treatments, and microbial use of six categories of substrates significantly decreased in both layers after biochar addition, although the use of amines and amides did not differ amongst the three treatments in the deeper layer. Maize above ground dry biomass and height did not differ significantly amongst the treatments, and biochar had no significant effect on nitrogen uptake by maize seedlings. H was positively correlated with AWCD, and negatively with pH. AWCD was positively correlated with mineral N and negatively with pH. Our results indicated that shifts in soil microbial functional diversity affected by biochar were not effective indicators of soil quality in earlier maize growth periods in this region.

Addition of Rubber to soil damages the functional diversity of soil.

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Soil microbial biomass and functional diversity in shrub-encroached grasslands along a precipitation gradient

The use of soil microbial and biochemical parameters could play an important role in monitoring effects of shrub encroachment in grasslands due to their rapid reaction to environmental fluctuations. We compared total organic carbon (Corg), soil total nitrogen (TON), microbial biomass, basal respiration, soil microbial quotient (Cmic/Corg) species and functional diversity between pairs of neighbouring, leguminous shrub-encroached and open grassland plots along a rainfall gradient (300mm to 1500mm mean annual precipitation (MAP)) in South Africa. "In semi-arid regions, soil Corg was higher in shrub-encroached grasslands than in open grasslands while the reverse was true in humid regions (1500 mm MAP)". Soil total nitrogen was generally higher in the shrub-encroached grasslands compared to open grasslands. Soil microbial biomass and basal respiration was higher in shrub-encroached grassland across the precipitation gradient. There was also a difference in microbial functional diversity between the encroached and adjacent open grasslands, which was most evident in the semi-arid regions. Our results suggest that land-cover change might influence microbial properties along the rainfall gradient.

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.

Microbial community diversity and the interaction of soil under maize growth in different cultivation techniques

Soil microbial functional diversity under maize grown in different agricultural management practices was determined using the Biolog EcoPlates and other microbial and biochemical methods. Comparisons of substrate utilization and the diversity indices showed differences in community composition of microorganisms related to different cultivation techniques and seasons. The soil samples collected in spring were characterized by statistically significant lower indices of biological activity in comparison to the soil collected from the flowering stage of maize. The soils collected in spring from the plots with full tillage had a similarly high biological activity as the soils obtained from maize flowering season. The principal component of PC analysis, showed the strong correlation between the parameters of soil quality and biodiversity indicators. Selected indicators of soil microbial diversity explained 71.51% of biological variability in soils. Based on the PC analysis, two major groups of soils have been indicated. Management practices and seasons were two important factors affecting soil microbial communities.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture.

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation.

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Increasing crop diversity increased soil microbial activity, nitrogen-sourcing and crop nitrogen, but not soil microbial diversity

The relationships between crop diversity, soil microbial diversity and agroecosystem functioning are not well understood. Soils under wheat monoculture, wheat–medic, and wheat–medic plus clover rotations from a 19-year-old wheat rotation trial in South Africa were measured for soil microbial functional and genetic diversity using community-level physiological profiling and automated rRNA intergenic spacer analysis. A 15N–13C dual isotope mixing model determined the nitrogen (N) sourcing when wheat was supplied with N from fertiliser and sheep dung (monoculture), or fertiliser, diazotrophy from one or two legumes, and sheep dung (wheat in rotation). Historical wheat yields and foliar [N] were 28% and 106% higher in wheat–legume rotations compared with wheat monoculture. Increasing crop diversity was related to increased soil microbial activity, but not increased microbial richness or diversity, which depended more on known abiotic drivers of microbial community structure. The δ15N mixing models revealed an increasing dependence on legume-derived N with increasing legume species in rotation. This suggests that enhanced N cycling and yield in crop–legume rotations is not a result of microbial diversity per se, but rather increased microbial activity when keystone legume species and their associated N2-fixing symbionts were present.

Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest.

Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.

Effect of Bioaugmentation by Bacterial Consortium and Methyl-β-cyclodextrin on Soil Functional Diversity and Removal of Polycyclic Aromatic Hydrocarbons

ABSTRACTThe low biological effectiveness of polycyclic aromatic hydrocarbons (PAHs) is the main limiting factor of in-situ bioremediation of PAH-contaminated soil. The purpose of the present study was to assess the effects of methyl-β-cyclodextrin (MCD) and microbial consortia on the PAHs degradation rate and microbial ecology and functional diversity and stability in soil. The results show that MCD and microorganisms significantly increased the degradation rate of pyrene and benzo[a]pyrene by 30.1% and 9.1%, respectively, (p < 0.05) after 4 weeks. The average well color development (AWCD) values and diversity indices of bioaugmentation (B) and MCD- and bacterial-assisted bioaugmentation (MB) were significantly higher than that in control (CK). The Shannon–Weaver index (H) and McIntosh index (U) in the MB treatment were significantly higher than those observed in other treatments, which indicated that its species richness and individuals were distributed evenly. The soil microbial activity and community structure were the most abundant in the MB treatment. Compared to the CK treatment, MB significantly promoted soil dehydrogenase activity (DHA) and fluorescein diacetate hydrolysis (FDAH) enzyme activity, which were increased by 96.3% and 994.3%, respectively. According to the results of principal component analysis, the physiological functions of microbial communities in the MB and B treatments were different from the other treatments. Therefore, the combination of the microorganisms with MCD can stimulate the remediation efficiency of PAHs and the physiological functions of microbial communities.

Responses of absolute and specific enzyme activity to consecutive application of composted sewage sludge in a Fluventic Ustochrept.

Composted sewage sludge (CS) is considered a rich source of soil nutrients and significantly affects the physical, chemical, and biological characteristics of soil, but its effect on specific enzyme activity in soil is disregarded. The present experiment examined the absolute and specific enzyme activity of the enzymes involved in carbon, nitrogen, and phosphorus cycles, the diversity of soil microbial functions, and soil community composition in a Fluventic Ustochrept under a maize—wheat rotation system in North China during 2012–2015. Application of CS led to increase in MBC and in its ratio to both total organic carbon (TOC) and microbial biomass nitrogen (MBN). Absolute enzyme activity, except that of phosphatase, increased in CS-treated soils, whereas specific activity of all the enzymes declined, especially at the highest dose of CS (45 t ha−1). The diversity of soil microbial community also increased in CS-treated soils, whereas its functional diversity declined at higher doses of CS owing to the lowered specific enzyme activity. These changes indicate that CS application induced the domination of microorganisms that are not metabolically active and those that use resources more efficiently, namely fungi. Redundancy analysis showed that fundamental alterations in soil enzyme activity depend on soil pH. Soil specific enzyme activity is affected more than absolute enzyme activity by changes in soil properties, especially soil microbial activity and composition of soil microflora (as judged by the following ratios: MBC/TOC, MBC/MBN, and TOC/LOC, that is labile organic carbon) through the Pearson Correlation Coefficient. Specific enzyme activity is thus a more accurate parameter than absolute enzyme activity for monitoring the effect of adding CS on the activities and structure of soil microbial community.

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau

Previous studies have explored the effects of global change on above-ground vegetation in grassland ecosystems. Few, however, have investigated the responses of root dynamics and soil microbes to simulated warming in alpine meadows of the Qinghai-Tibet Plateau. This research used field open top chamber experiment to examine warming's impacts. Root production, mortality, and turnover were observed in situ using minirhizotron tubes, while soil microbial community composition and diversity were assessed by using phospholipid-derived fatty acids (PLFA) and Biolog-Eco plates. The results showed that 1) warming shifted the root standing crop distribution to deeper soil while increasing the accumulated root mortality and root production at 0–10cm soil depth; 2) warming increased the abundance of fungal PLFAs while decreasing the abundance of other functional groups; 3) warming decreased the soil microbial functional diversity at the different soil layers; 4) bacterial and fungal PLFA contents were positively correlated with root mortality and turnover but were negatively correlated with root standing crop; 5) root dynamics significantly affect carbon utilization of the soil microbial community; and warming induced changes in root dynamics are associated with soil microbial community structure and function. Overall, these findings indicate that warming alters root production, mortality, and turnover and the relative abundance of different microorganisms in different soil layers. As a result, warming tended to shift microbial communities from bacteria toward fungi, leading to changes in the microbial community structure in different soil layers.

Ecotoxicological Assessment of Chemical Fumigants Utilising an Earthworm (Eisenia andrei) Bioassay and Soil Microbial Communities

Fumigation is an important crop protection practice employed to control soil pathogens and diseases. Metham sodium and cadusafos are two commonly used soil fumigants for this purpose. However, little information is available on their effects on non-target soil organisms. The aim of the study was to determine the ecotoxicity of these chemical fumigants on earthworms (organismal responses and DNA damage) and soil microbial communities. Changes in soil microbial community function and structure were evaluated by means of Biolog™ Ecoplates and phospholipid fatty acid (PLFA) analyses, respectively. Both fumigants had a significant (p < 0.05) negative impact on all earthworm endpoints. Earthworms did not reproduce; biomass was affected negatively and manifested significant DNA damage with metham sodium causing more pronounced effects in comparison to cadusafos. The fumigants had an inhibitory effect on microbial growth. No lasting effects were observed in the community structure but cadusafos had a pronounced effect on the microbial community functional diversity. Metham sodium and cadusafos had varying effects on earthworm and microbial endpoints. This illustrates the importance of using different bioindicators to get a better understanding of the overall effects on the soil ecosystem.

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar

Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar.

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows

Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival. Data regarding the identity and abundance of bacterial genes governing traits such as virulence, antibiotic resistance, and stress responses could enable identification of previously unknown agents that play a role in metritis pathogenesis. Moreover, such knowledge could lead to the development of improved treatments or preventive methods. Therefore, the objectives of this study were to characterize the uterine microbial population and to differentiate, for the first time, the microbial functional diversity in cows with metritis versus healthy cows. In addition, we aimed to identify relationships between microbial genes and postpartum uterine health. Uterine swabs were collected from 24 cows within 3 to 12 d in milk; 12 cows were diagnosed with metritis and the other 12 were healthy. Metritis was defined as a watery, reddish or brownish uterine discharge having a fetid smell, and rectal temperature greater than 39.5°C. Cows with a clear and viscous uterine discharge, not fetid or mucopurulent, were classified as healthy. Microbial metagenomic DNA from uterine swab samples was subjected to whole-genome shotgun sequencing on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). The MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/) and STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) were used to detect statistically significant differences in the abundance of taxonomic and functional features between the uterine microbial metagenomes of metritic and healthy cows. Our results showed an increased abundance of Fusobacteria and Bacteroidetes in metritic cows, confirming the potential role of those 2 taxa in the pathogenesis of metritis. The MG-RAST analysis revealed a significantly higher abundance of genes for protein transport across the cytoplasmic membrane and type VI bacterial secretion systems in the metritic microbiota. Additionally, genes coding for resistance to acid stress were exclusive to the metritis microbiota, suggesting that microbial resistance to acid stress is important for microbial survival in the infected uterus. On the other hand, genes coding for adhesion molecules, bacteriocins, and antibacterial peptides were significantly associated with the uterine microbiota of healthy cows, as was tolerance to colicin E2.

Metagenomic analysis of the microbiome in three different bioreactor configurations applied to commercial laundry wastewater treatment

The taxonomic and functional diversity of three different biological reactors (fluidized bed reactor, FBR; up-flow anaerobic sludge blanket reactor, UASB; and expanded granular sludge bed reactor, EGSB) used for commercial laundry wastewater treatment was investigated using metagenome shotgun sequencing. Metagenomes were sequenced on the Illumina Hiseq platform and were analyzed using MG-RAST, STAMP and PAST software. The EGSB and UASB reactors were more closely related based on taxonomic and functional profiles, likely due to similar granular sludge and procedures adopted to ensure anaerobic conditions. The EGSB and UASB reactors showed a predominance of methanogens and genes related to methanogenesis, with a prevalence of the acetoclastic pathway, in addition to the peripheral and central O2-independent pathways for aromatic compound degradation. By contrast, FBR showed a dominance of aerobic microbiota and pathways for O2-dependent aromatic compound degradation. Therefore, although the reactors showed similar surfactant removal levels, the microbial composition, functional diversity and aromatic compound degradation pathways were significantly distinct.