Patterns of substrate utilization during long-term incubations at different temperatures

Microorganisms play key roles in biogeochemical cycling by facilitating the release of nutrients from organic compounds. In doing so, microbial communities use different organic substrates that yield different amounts of energy for maintenance and growth of the community. Carbon utilization efficiency (CUE) is a measure of the efficiency with which substrate carbon is metabolized versus mineralized by the microbial biomass. In the face of global change, we wanted to know how temperature affected the efficiency by which the soil microbial community utilized an added labile substrate, and to determine the effect of labile soil carbon depletion (through increasing duration of incubation) on the community's ability to respond to an added substrate. Cellobiose was added to soil samples as a model compound at several times over the course of a long-term incubation experiment to measure the amount of carbon assimilated or lost as CO2 respiration. Results indicated that in all cases, the time required for the microbial community to take up the added substrate increased as incubation time prior to substrate addition increased. However, the CUE was not affected by incubation time. Increased temperature generally decreased CUE, thus the microbial community was more efficient at 15 degrees C than at 25 degrees C. These results indicate that at warmer temperatures microbial communities may release more CO2 per unit of assimilated carbon. Current climate-carbon models have a fixed CUE to predict how much CO2 will be released as soil organic matter is decomposed. Based on our findings, this assumption may be incorrect due to variation of CUE with changing temperature. (c) 2008 Elsevier Ltd. All rights reserved.

Culture independent analysis of greyback canegrub-associated microflora and microbial community comparison using subtractive hybridisation

Greyback canegrubs cost the Australian sugarcane industry around $13 million per annum in damage and control. A novel and cost effective biocontrol bacterium could play an important role in the integrated pest management program currently in place to reduce damage and control associated costs. During the course of this project, terminal restriction fragment length polymorphism (TRFLP), 16-S rDNA cloning, suppressive subtractive hybridisation (SSH) and entomopathogen-specific PCR screening were used to investigate the little studied canegrub-associated microflora in an attempt to discover novel pathogens from putatively-diseased specimens. Microflora associated with these soil-dwelling insects was found to be both highly diverse and divergent between individual specimens. Dominant members detected in live specimens were predominantly from taxa of known insect symbionts while dominant sequences amplified from dead grubs were homologous to putativelysaprophytic bacteria and bacteria able to grow during refrigeration. A number of entomopathogenic bacteria were identified such as Photorhabdus luminescens and Pseudomonas fluorescens. Dead canegrubs prior to decomposition need to be analysed if these bacteria are to be isolated. Novel strategies to enrich putative pathogen-associated sequences (SSH and PCR screening) were shown to be promising approaches for pathogen discovery and the investigation of canegrubsassociated microflora. However, due to inter- and intra-grub-associated community diversity, dead grub decomposition and PCR-specific methodological limitations (PCR bias, primer specificity, BLAST database restrictions, 16-S gene copy number and heterogeneity), recommendations have been made to improve the efficiency of such techniques. Improved specimen collection procedures and utilisation of emerging high-throughput sequencing technologies may be required to examine these complex communities in more detail. This is the first study to perform a whole-grub analysis and comparison of greyback canegrub-associated microbial communities. This work also describes the development of a novel V3-PCR based SSH technique. This was the first SSH technique to use V3-PCR products as a starting material and specifically compare bacterial species present in a complex community.

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO 2-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH 4-N, CO 2-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns.

What is the available evidence concerning relative performance of different designs of mixed-species plantings for smallholder and community forestry in the tropics? A systematic map protocol

Background There has been growing interest in mixed species plantation systems because of their potential to provide a range of socio-economic and bio-physical benefits which can be matched to the diverse needs of smallholders and communities. Potential benefits include the production of a range of forest products for home and commercial use; improved soil fertility especially when nitrogen fixing species are included; improved survival rates and greater productivity of species; a reduction in the amount of damage from pests or disease; and improved biodiversity and wildlife habitats. Despite these documented services and growing interest in mixed species plantation systems, the actual planting areas in the tropics are low, and monocultures are still preferred for industrial plantings and many reforestation programs because of perceived higher economic returns and readily available information about the species and their silviculture. In contrast, there are few guidelines for the design and management of mixed-species systems, including the social and ecological factors of successful mixed species plantings. Methods This protocol explains the methodology used to investigate the following question: What is the available evidence for the relative performance of different designs of mixed-species plantings for smallholder and community forestry in the tropics? This study will systematically search, identify and describe studies related to mixed species plantings across tropical and temperate zones to identify the social and ecological factors that affect polyculture systems. The objectives of this study are first to identify the evidence of biophysical or socio-economic factors that have been considered when designing mixed species systems for community and smallholder forestry in the tropics; and second, to identify gaps in research of mixed species plantations. Results of the study will help create guidelines that can assist practitioners, scientists and farmers to better design mixed species plantation systems for smallholders in the tropics.

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.