What Impact Does Sustainable Certification Have? A Comparison of Aquatic Nitrate and Phosphate Levels between Two Golf Courses in the Bloomington-Normal Community

Two golf courses in the Bloomington-Normal community in central Illinois were tested for nitrate and phosphate concentrations in their ponds. One golf course (The Den) is Audubon International certified while the other golf course (Ironwood) is not. This study tries to establish if differing environmental management practices can contribute to significantly different concentrations of nutrients. It was determined that the nitrate concentration was higher at the non-certified golf course, while the phosphate concentrations at both courses were essentially negligible. The implications of these findings are discussed and were presented to both golf courses. It is the hope of this paper that the non-certified golf course will seek improved management practices, with regard to environmental impact, after observing the differences in nutrient concentrations

Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A

Immunoglobulin A (IgA) is prominently secreted at mucosal surfaces and coats a fraction of the intestinal microbiota. However, the commensal bacteria bound by IgA are poorly characterized and the type of humoral immunity they elicit remains elusive. We used bacterial flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in murine models of immunodeficiency to identify IgA-bound bacteria and elucidate mechanisms of commensal IgA targeting. We found that residence in the small intestine, rather than bacterial identity, dictated induction of specific IgA. Most commensals elicited strong T-independent (TI) responses that originated from the orphan B1b lineage and from B2 cells, but excluded natural antibacterial B1a specificities. Atypical commensals including segmented filamentous bacteria and Mucispirillum evaded TI responses but elicited T-dependent IgA. These data demonstrate exquisite targeting of distinct commensal bacteria by multiple layers of humoral immunity and reveal a specialized function of the B1b lineage in TI mucosal IgA responses

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

BACKGROUND: Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with the intestinal mucosa. Biopsies disrupt the epithelium and can be associated with complications such as bleeding. Biopsies sample a limited area of the mucosa, which can lead to potential sampling bias. In contrast to the mucosal biopsy, the mucosal brush technique is less invasive and provides greater mucosal coverage, and if it can provide equivalent microbial community data, it would be preferable to mucosal biopsies. RESULTS: We compared microbial samples collected from the intestinal mucosa using either a cytology brush or mucosal biopsy forceps. We collected paired samples from patients with ulcerative colitis (UC) who had previously undergone colectomy and ileal pouch anal anastomosis (IPAA), and profiled the microbial communities of the samples by sequencing V4-V6 or V4-V5 16S rRNA-encoding gene amplicons. Comparisons of 177 taxa in 16 brush-biopsy sample pairs had a mean R(2) of 0.94. We found no taxa that varied significantly between the brush and biopsy samples after adjusting for multiple comparisons (false discovery rate ≤0.05). We also tested the reproducibility of DNA amplification and sequencing in 25 replicate pairs and found negligible variation (mean R(2) = 0.99). A qPCR analysis of the two methods showed that the relative yields of bacterial DNA to human DNA were several-fold higher in the brush samples than in the biopsies. CONCLUSIONS: Mucosal brushing is preferred to mucosal biopsy for sampling the epithelial-associated microbiota. Although both techniques provide similar assessments of the microbial community composition, the brush sampling method has relatively more bacterial to host DNA, covers a larger surface area, and is less traumatic to the epithelium than the mucosal biopsy

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Background: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. Findings: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Conclusions: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative

Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis

Dysbiosis resulting in gut-microbiome alterations with reduced butyrate production are thought to disrupt intestinal immune homeostasis and promote complex immune disorders. However, whether and how dysbiosis develops before the onset of overt pathology remains poorly defined. Interleukin-15 (IL-15) is upregulated in distressed tissue and its overexpression is thought to predispose susceptible individuals to and have a role in the pathogenesis of celiac disease and inflammatory bowel disease (IBD). Although the immunological roles of IL-15 have been largely studied, its potential impact on the microbiota remains unexplored. Analysis of 16S ribosomal RNA-based inventories of bacterial communities in mice overexpressing IL-15 in the intestinal epithelium (villin-IL-15 transgenic (v-IL-15tg) mice) shows distinct changes in the composition of the intestinal bacteria. Although some alterations are specific to individual intestinal compartments, others are found across the ileum, cecum and feces. In particular, IL-15 overexpression restructures the composition of the microbiota with a decrease in butyrate-producing bacteria that is associated with a reduction in luminal butyrate levels across all intestinal compartments. Fecal microbiota transplant experiments of wild-type and v-IL-15tg microbiota into germ-free mice further indicate that diminishing butyrate concentration observed in the intestinal lumen of v-IL-15tg mice is the result of intrinsic alterations in the microbiota induced by IL-15. This reconfiguration of the microbiota is associated with increased susceptibility to dextran sodium sulfate-induced colitis. Altogether, this study reveals that IL-15 impacts butyrate-producing bacteria and lowers butyrate levels in the absence of overt pathology, which represent events that precede and promote intestinal inflammatory diseases

Assessing restoration potential in relict wetland soils: investigating the effect of wetland hydrology on soil microbial community composition and denitrification potential

Microbial communities are known to strongly influence rates of biogeochemical cycling in wetland ecosystems; specifically, they are strong determinants of rates of denitrification typically observed. Human induced land use changes have significantly reduced the acreage of wetland habitats, with dam building in the eastern United States figuring prominently in these losses. Wetlands located behind these dams turned into ponds, and this ecosystem alteration significantly lowers denitrification potential. Due to these ecosystem land use changes, higher exports of anthropogenic nitrate continue to leach off the land, ultimately ending up in open bodies of water. The damming and subsequent ponding of these floodplain systems have caused radically altered environmental conditions for relict wetland soils. Microbial communities are resistant to change, and may undergo periods of dormancy when conditions are not conducive to activity, but it is uncertain how long they can withstand the effects of ecosystem alteration. By removing the dam and the depositional sediments, wetland restoration efforts attempt to stimulate higher rates of denitrification observed at the site. However, understanding if the microbial community inhabiting the relict hydric soil has a high restoration potential (e.g., capability of performing higher rates of denitrification when wetland hydrology is returned) is important when studying sites targeted for restoration. This thesis attempts to address wetland restoration potential with two studies. In the first part, the hydric soil from Big Spring Run (a site targeted for wetland restoration) was surveyed for both denitrification potential and microbial community composition. Big Spring Run (BSR) was the site of a floodplain wetland prior to European settlement; however, in the 1800s, a dam was erected downstream, filling the wetland to create a mill pond. The dam was removed in the mid-1900s; however the relict wetland soil remained buried under settled pond sediments. The relict wetland soil at BSR was surveyed to see if the microbial communities present in the relict hydric soil (which has been buried for over 200 years) are still functional. Results indicate that the current buried hydric soil performs denitrification at significantly lower rates than any of the surveyed reference wetlands (Nov 2010 F[4,31] = 13.75, p<0.0001; March 2011 F[4,42] = 84.6, p<0.0001; June 2011 F[4,35] = 71.89, p<0.0001). Bacterial community composition was also distinct between all of the sites sampled (ANOSIM R=0.693, p<0.001) indicating that no specific community composition is needed to perform denitrification. The second part of this thesis attempts to determine if the microbial community contained within relict hydric soil will perform high rates of denitrification again ii when dynamic wetland hydrology is restored. Soil from the altered BSR site was transplanted to nearby wetland ecosystems and denitrification rates and microbial community composition were assessed before and after transplanting. Results indicate that when stable wetland environmental parameters dominate, the microbial communities perform higher rates of denitrification in the transplanted sites than in their current altered conditions (F[5,66]= 8.459, p<0.0001). However these denitrification rates, while improved over their current conditions, are still significantly lower than any of the surveyed reference wetland sites. Results were mixed when other environmental parameters (e.g., cold temperatures, persistent flooding, and high stream flow) affected the results. Further work is needed to test the long term implications of these findings; however the preliminary results indicate that while the hydric soil microbial communities do show slight improvements in denitrification potential after transplanting, the soil microbial community at BSR seems resistant to a full recovery of denitrifying potential