Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Biological soil crust is composed of lichens, cyanobacteria, green algae, mosses, and fungi. Although crusts are a dominant source of nitrogen (N) in arid ecosystems, this study is among the first to demonstrate their contribution to N availability in xeric temperate habitats. The study site is located in Lucas County of Northwest Ohio. Using an acetylene reduction technique, we demonstrated potential N fixation for these crusts covering sandy, acidic, low N soil. Similar fixation rates were observed for crust whether dominated by moss, lichen, or bare soil. N inputs from biological crusts in northwestern Ohio are comparable to those in arid regions, but contribute substantially less N than by atmospheric deposition. Nitrate and ammonium leaching from the crust layer were quantified using ion exchange resin bags inserted within intact soil cores at 4 cm depth. Leaching of ammonium was greater and nitrate less in lichen than moss crusts or bare soil, and was less than that deposited from atmospheric sources. Therefore, biological crusts in these mesic, temperate soils may be immobilizing excess ammonium and nitrate that would otherwise be leached through the sandy soil. Moreover, automated monitoring of microclimate in the surface 7 cm of soil suggests that moisture and temperature fluctuations in soil are moderated under crust compared to bare soil without crust. We conclude that biological crusts in northwestern Ohio contribute potential N fixation, reduce N leaching, and moderate soil microclimate.

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Infections of the cow udder leading to mastitis and reducing milk quality are a critical challenge facing all dairy farmers. Mastitis may be linked to the ecological disruption of an endogenous mammary microbial community, suggesting an ecosystems approach to management and prevention of this disease. The teat end skin represents a first point of host contact with mastitis pathogens and may offer an opportunity for microbially mediated resistance to infection, yet we know little about the microbial community of teat end skin or its potential interaction with the microbial community of intramammary milk of organic dairy cattle. High-throughput sequencing of marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected gland (i.e., udder quarter) and to assess the sharing of microbial DNA between these tissue habitat sites. The mammary microbiome varied among cows, through time, and between skin and milk. Microbiomes of milk from healthy and infected quarters reflected a diverse group of microbial DNA sequences, though milk had far fewer operational taxonomic units (OTUs) than skin. Milk microbiomes of infected quarters were generally more variable than healthy quarters and were frequently dominated by a single OTU; teat end skin microbiomes were relatively similar between healthy and infected quarters. Commonly occurring genera that were shared between skin and milk of infected glands included Staphylococcus spp. bacteria and Debaryomyces spp. fungi. Commonly occurring genera that were shared between skin and milk of healthy glands included bacteria SMB53 (Clostridiaceae) and Penicillium spp. fungi. Results support an ecological interpretation of the mammary gland and the notion that mastitis can be described as a dysbiosis, an imbalance of the healthy mammary gland microbiome.

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Aims The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources. Method and Results Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH4‐N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful. Conclusions Dairy‐based composts are less likely to support E. coli survival than poultry‐based composts. Significance and Impact of the Study Results aid in risk assessment of the use of different types of manure‐based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.

Summary 1.We tested the effects of elevated concentrations of atmospheric CO 2 on herbivorous nematodes in soil supporting plantations of Loblolly Pine ( Pinus taeda ) or Sweet Gum ( Liquidambar styraciflua ) trees in FACE experiments in the Eastern USA. We expected any net increase in carbon allocation to the rhizosphere to increase the abundance, biomass or respiration of the nematode community. 2. Data were analysed with effect of CO 2 concentration nested within month and year to isolate the maximum potential effect of CO 2 treatment on soil nematode communities. 3. Elevated CO 2 decreased total abundance of nematodes in both forests, but impacts were greater in Sweet Gum than Loblolly Pine forests. Soil nematode community respiration and biomass increased with elevated CO 2 in Loblolly Pine, but decreased with fumigation in Sweet Gum forests. 4. Fungivores were the only trophic group showing a consistent response at both sites, with reduced abundance, biomass and respiration at elevated CO 2 . 5. Estimated total respiration of soil nematode communities ranged from 2·9-11·2 g C m − 2 year − 1 in Pine soils and 0·6-4·7 g C m − 2 year − 1 in Sweet Gum soils, representing ≤ 1% of net primary production in these forests. 6. Our results indicate that effects of elevated CO 2 on soil nematode communities will not necessarily have a simple functional relationship with rhizosphere carbon allocation.

We evaluated the potential of soil microarthropods and enchytraeid worms to be useful as bioindicators of soil condition in forest, wetland, and agricultural ecosystems over a range of ecoregions. Selected mesofauna and soil characteristics in soil and litter in relatively undisturbed and disturbed examples of each of three ecosystems within each of three land resource regions were monitored over two years. Optimal times of year to sample these organisms as indicators of disturbance were April, May, July and September. No single measure reflected disturbance across all three ecosystems. Among forest sites, Simpson's diversity index, evenness, abundance of ants, and proportion of enchytraeids in the mesofauna differed between soils of different disturbance levels. Among agricultural sites, richness, evenness, abundance of mites, and proportions of collembolans and of enchytraeids in the mesofauna differed between disturbance levels. Among wetland sites, Shannon's and Simpson's diversity indices, richness based on the total mesofauna, and abundances of mites, diplurans, ants, and isotomid and onychiurid collembolans differed between disturbance levels. Covariates most frequently associated with abundance and diversity of the measured mesofauna were soil electrical conductivity, available N, organic matter, and pH. Canonical correspondence analysis provided information somewhat different to bivariate analysis. Using both approaches to examine soil and litter taxa that have distinctive responses to disturbance may help to identify candidate groups applicable for use in large-scale environmental monitoring programs.