Effect of Soil Chemistry on Microbial Biodiversity and Functionality in Grassland and Tilled Soils

Microorganisms are excellent indicators of soil health, because of their rapid response to environmental change. Traditional microbiology is ineffective for the study of soil, as \u3c 1% of microorganisms are currently culturable (Torsvik et al., 1996). Nucleic acid based methods, however, allow rapid detection of organisms, or particular genes, directly from soil samples. This work investigated, using polymerase chain reaction (PCR)-based approaches, the relationship between key chemical properties and bacterial biodiversity in grassland and tilled soils, with particular emphasis on the abundance and diversity of ammonium oxidisers

Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

One of the most common approaches for investigating the ecology of spatially complex environments is to examine a single biotic assemblage present, such as macroinvertebrates. Underlying this approach are assumptions that sampled and unsampled taxa respond similarly to environmental gradients and exhibit congruence across different sites. These assumptions were tested for five benthic groups of various sizes (archaea, bacteria, microbial eukaryotes/protists, meiofauna and macrofauna) in Plymouth Sound, a harbour with many different pollution sources. Sediments varied in granulometry, hydrocarbon and trace metal concentrations. Following variable reduction, canonical correspondence analysis did not identify any associations between sediment characteristics and assemblage composition of archaea or macrofauna. In contrast, variation in bacteria was associated with granulometry, trace metal variations and bioturbation (e.g. community bioturbation potential). Protists varied with granulometry, hydrocarbon and trace metal predictors. Meiofaunal variation was associated with hydrocarbon and bioturbation predictors. Taxon turnover between sites varied with only three out of 10 group pairs showing congruence (meiofauna-protists, meiofauna-macrofauna and protists-macrofauna). While our results support using eukaryotic taxa as proxies for others, the lack of congruence suggests caution should be applied to inferring wider indicator or functional interpretations from studies of a single biotic assemblage

DNA extraction method affects microbial community profiles from soils and sediment

To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types

Fate of trace metals in anaerobic digestion

© Springer International Publishing Switzerland 2015. A challenging, and largely uncharted, area of research in the field of anaerobic digestion science and technology is in understanding the roles of trace metals in enabling biogas production. This is a major knowledge gap and a multifaceted problem involving metal chemistry; physical interactions of metal and solids; microbiology; and technology optimization. Moreover, the fate of trace metals, and the chemical speciation and transport of trace metals in environments— often agricultural lands receiving discharge waters from anaerobic digestion processes— simultaneously represents challenges for environmental protection and opportunities to close process loops in anaerobic digestion.The authors acknowledge funding within the framework of the COST Action 1302 (‘European Network on Ecological Roles of Trace Metals in Anaerobic Biotechnologies’). GC is supported by a European Research Council Starting Grant (‘3C-BIOTECH; No. 261330).Peer Reviewe

Abundance of denitrification genes under different peizometer depths in four Irish agricultural groundwater sites

This study examined the relationship between the abundance of bacterial denitrifiers in groundwater at four sites, differing with respect to overlaying land management and peizometer depth. Groundwater was sourced from 36 multilevel piezometers, which were installed to target different groundwater zones: (1) subsoil, (2) subsoil to bedrock interface, and (3) bedrock. The gene copy concentrations (GCCs), as gene copies per liter, for bacterial 16S rRNA genes and the denitrifying functional genes, nirK, nirS, and nosZ, were determined using quantitative polymerase chain reaction assays. The results were related to gaseous nitrogen emissions and to the physicochemical properties of the four sites. Overall, nirK and nirS abundance appeared to show no significant correlation to N2O production (P = 0.9989; P = 0.3188); and no significant correlation was observed between nosZ and excess N2 concentrations (P = 0.0793). In the majority of piezometers investigated, the variation of nirK and nirS gene copy concentrations was considered significant (P < 0.0001). Dissolved organic carbon (DOC) decreased with aquifer depth and ranged from 1.0-4.0 mg l-1, 0.9-2.4 mg l-1, and 0.8-2.4 mg l-1 within piezometers located in the subsoil, subsoil/bedrock interface, and bedrock depths, respectively. The availability of increasing DOC and the depth of the water table were positively correlated with increasing nir and nosZ GCCs (P = 0.0012). A significant temporal correlation was noted between nirS and piezometer depth (P < 0.001). Interestingly, the nirK, nirS, and nosZ GCCs varied between piezometer depths within specific sites, while GCCs remained relatively constant from site to site, thus indicating no direct impact of agricultural land management strategies investigated on denitrifier abundance.close