Geogenic factors as drivers of microbial community diversity in soils overlying polymetallic deposits

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P 0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The effect of bacteria on the sensitivity of microalgae to copper in laboratory bioassays

Although single-species laboratory toxicity tests with microalgae are sensitive and highly reproducible, they lack environmental realism. Interactions between algae and their associated bacteria, either in the plankton or in biofilms, may alter algal sensitivity to contaminants, which are not mimicked in laboratory toxicity tests. This study investigated the effects of simple algal-bacterial relationships on the sensitivity of laboratory-cultured algae to copper using 72-h algal growth-rate inhibition bioassays. Four species of microalgae were used, two isolates of each; a strain of algae with no microscopically visible and no culturable bacteria present (operationally defined as axenic) and a non-axenic strain. The four algae used were the marine diatom Nitzschia closterium, the freshwater green alga Pseudokirchneriella subcapitata and two tropical Chlorella spp. Under control conditions (no copper), N. closterium and P. subcapitata grew better in the presence of the bacterial community. Sensitivity to copper (assessed as the concentration to inhibit the growth rate by 50% after 72-h (IC50)) was not significantly different for the axenic and non-axenic strains of N. closterium, P. subcapitata or for Chlorella sp. (PNG isolate). At pH 5.7, the axenic Chlorella sp. (NT isolate) had a 72-h IC50 of 46 μg Cu L−1, while in the presence of bacteria the IC50 increased (i.e., sensitivity decreased) to 208 μg Cu L−1. However, when the bacterial status of both the operationally defined axenic and non-axenic cultures of N. closterium and Chlorella sp. (NT isolate) was investigated using polymerase chain reaction (PCR) amplification of 16S rRNA followed by DNA fingerprinting using denaturing gradient gel electrophoresis (DGGE), it was found that bacteria were actually present in all the algal cultures, i.e. the axenic cultures were not truly bacteria-free. Based on sequence information, the bacteria present were nearly all identified as alphaproteobacteria, and a number of isolates had high similarity to bacteria previously identified as symbionts or species endophytically associated with marine organisms. The “axenic” cultures contained less bacterial phylotypes than the non-axenic cultures, and based on band-intensity, also contained less bacterial DNA. This supported the findings of few differences in copper sensitivity between strains, and suggests that standard microalgal toxicity tests probably inadvertently use non-axenic cultures in metal assessment

The effect of field-collected biofilms on the toxicity of copper to a marine microalga (Tetraselmis sp.) in laboratory bioassays

Standard algal growth rate inhibition bioassays can lack environmental realism and may over- or underestimate metal bioavailability in natural systems. In aquatic environments, algal species interact with other biota, including other algae, bacteria and biofilms. In this work, the feasibility of incorporating marine biofilms into 72h algal growth inhibition toxicity tests was explored. The effects of copper on Tetraselmis sp. were tested in the absence and presence of characterised field-collected biofilms. We hypothesised that the addition of biofilm would prevent copper toxicity to the alga primarily through interactions of the metal with other cells and biofilm exudates. The sensitivity of Tetraselmis sp. to copper (based on 72h IC50 values; the copper concentration to inhibit population growth by 50%) in the presence of a blended biofilm inoculum varied 2-fold and was independent of the amount of biofilm added. However, increases in IC10 and IC20 values indicated some amelioration of copper toxicity. When intact biofilms were added to the bioassays, amelioration of toxicity was more consistent, probably due to increased binding of copper to cell surfaces or exudates. Difficulties in characterising biofilms and distinguishing that material from the test alga need to be overcome before biofilms can be routinely incorporated into laboratory bioassays

Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow▿

We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (P < 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including Oceanospirillales and Methylococcaceae. 16S rRNA gene sequences from less-disturbed sites had representatives of the Caulobacteraceae, Sphingomonadaceae, and Nitrospirae which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (P < 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (P < 0.05). The abundance of amoA, narG, and nifH genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N

The Abundance of Microbial Functional Genes in Grassy Woodlands Is Influenced More by Soil Nutrient Enrichment than by Recent Weed Invasion or Livestock Exclusion▿

A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory. Second, using quantitative real-time PCR, we investigated whether microbial nitrogen functional gene (NFG) abundance was altered with soil nutrient enrichment, livestock exclusion, and exotic grass invasion. The target genes were chiA (decomposition-ammonification), nifH (nitrogen fixation), nirK and narG (denitrification), and bacterial amoA (nitrification). Woodland soils were enriched in phosphorus and nitrogen compared to reference condition sites, but soil nutrients were not lower following livestock exclusion. Total nitrogen and nifH were negatively correlated in grazed woodlands, suggesting that aboveground herbivory reduces the capacity for belowground nitrogen fixation. Woodlands dominated by exotic grasses had higher levels of nitrate, narG, and nirK than those dominated by native grasses. We hypothesize that the increase in potential for denitrification was due to increases in soil nitrate, rather than changes in plant composition. Overall, soil physicochemistry explained more variation in NFG abundance than livestock presence or plant invasion, particularly for chiA and bacterial amoA, with significant relationships between the abundance of all five NFGs and total nitrogen or nitrate. All woodlands investigated had a history of anthropogenic disturbance and nutrification, and soil nutrient levels and the abundance of NFGs are likely to be related to long-term land management practices

Bacterial community structure and denitrifier (nir-gene) abundance in soil water and groundwater beneath agricultural land in tropical North Queensland, Australia

We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05),\ud particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P < 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NOforming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater\ud discharges lower in the GBR catchment zones

Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness

The microbiome of grassland soils provides ecosystem services essential to plant health and productivity, including nutrient cycling and suppression of soil-borne diseases. Understanding how soil management practices affect soil microbial communities will provide opportunities by which indigenous soil microbes and their functions can be managed to sustain or promote plant growth and enhance disease suppressiveness. Here, we investigated the impact of 20 years of plant residue management in a long-term grassland field trial on soil chemical and (micro)biological properties, in particular the suppression of damping-off disease of kale caused by the fungal root pathogen Rhizoctonia solani AG 2–1. Plant residue management led to significant variation in the community structure of the bacterial genus Pseudomonas between treatments. Soil organic matter quality (inferred carbon recalcitrance) was responsible for 80% of the observed variation in Pseudomonas community structure. Furthermore, increased Pseudomonas species diversity (Shannon's index), microbial activity, soil organic matter content, and carbon availability distinguished suppressive (low disease) soils from conducive (high disease) soils. More specifically, Pseudomonas species diversity and richness (Margalef's) were identified as the primary parameters explaining the greatest proportion (>30%) of variation in the disease suppressive capacity of soils across treatments. Collectively, our results suggest that management-induced shifts in Pseudomonas community composition, notably species diversity and richness, provide a better indicator of disease conduciveness for a broad-host range fungal pathogen than soil chemical parameters. In conclusion, our study indicates that frequent addition of organic residues to agricultural grassland soils enhances the diversity and activity of plant-beneficial bacterial taxa