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Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.

Biochar incorporated into soil has been known to affect soil nutrient availability and act as a habitat for microorganisms, both of which could be related to its particle size. However, little is known about the effect of particle size on soil microbial community structure and function. To investigate short-term soil microbial responses to biochar addition having varying particle sizes and addition rates, we established a laboratory incubation study. Biochar produced via pyrolysis of bamboo was ground into three particle sizes (diameter size<0.05mm (fine), 0.05-1.0mm (medium) and 1.0-2.0mm (coarse)) and amended at rates of 0% (control), 3% and 9% (w/w) in an intensively managed bamboo (Phyllostachys praecox) plantation soil. The results showed that the fine particle biochar resulted in significantly higher soil pH, electrical conductivity (EC), available potassium (K) concentrations than the medium and coarse particle sizes. The fine-sized biochar also induced significantly higher total microbial phospholipid fatty acids (PLFAs) concentrations by 60.28% and 88.94% than the medium and coarse particles regardless of addition rate, respectively. Redundancy analysis suggested that the microbial community structures were largely dependent of particle size, and that improved soil properties were key factors shaping them. The cumulative CO 2 emissions from biochar-amended soils were 2-56% lower than the control and sharply decreased with increasing addition rates and particle sizes. Activities of α-glucosidase, β-glucosidase, β-xylosidase, N-acetyl-β-glucosaminidase, peroxidase and dehydrogenase decreased by ranging from 7% to 47% in biochar-amended soils over the control, indicating that biochar addition reduced enzyme activities involved carbon cycling capacity. Our results suggest that biochar addition can affect microbial population abundances, community structure and enzyme activities, that these effects are particle size and rate dependent. The fine particle biochar may additionally produce a better habitat for microorganisms compared to the other particle sizes., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Viruses are highly abundant in soils with their numbers exceeding those of cooccurring bacterial cells by 10- to over 1000-fold. Water and organic matter content influence the magnitude of the viral-to-bacterial ratio in soils; thus, ecosystem type and land use shape interactions between viral and host microbial communities in soils. Less understood are the shorter term interactions between viral and host communities that ultimately maintain the large viral standing stock within soils. This study examined short-term dynamics of viral and bacterial communities in soils to determine whether the growth of soil bacterial communities results in the production of soil viruses, and if viral community responses occur within specific populations. In microcosms amended with different carbon sources, increases in viral abundance (VA) accompanied increases in bacterial abundance (BA) and bacterial respiration rate (BRR). The timing and intensity of increases in BA, VA and BRR were different across C sources suggesting differences in the predominant mode of viral replication within growth-stimulated bacterial populations. Moreover, compositional changes occurred in soil bacterial and viral communities indicating that new viral production arose from a subset of host populations. To our knowledge, these are the first observations of soil viral populations responding to short-term changes in soil bacterial communities., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.

Two studies were conducted to evaluate microbial populations in polycyclic aromatic hydrocarboncontaminated soil. Captina silt loam was freshly exposed to (1) 0 or 2000 mg pyrene/kg and sampled after 10- and 61-wk incubation and (2) 0 or 505 mg pyrene + 445 mg phenanthrene/kg and sampled after a 21-wk incubation. Microbial numbers were determined by plate-count techniques. Isolated bacteria, selected degraders, and wholesoil extracts were analyzed by fatty acid methyl ester analysis (FAME). In the pyrene experiment, pyrene did not affect total bacterial or fungal numbers, but pyrene degraders increased from undetectable levels to 7.09 log 10 degraders/g in the contaminated soil. The FAME analysis of bacterial isolates detected no pyrene effect, but wholesoil FAME indicated an increase in the contaminated soil of a fatty acid characteristic of protozoa and a major fatty acid detected in isolated degraders. In the pyrene + phenanthrene experiment, the contaminants had no impact on bacterial, fungal, or actinomycete numbers but increased degrader numbers. No effect of pyrene + phenanthrene was detected by isolate FAME, but whole-soil FAME indicated an effect similar to that in the pyrene experiment. The results indicate that pyrene, although not impacting microbial numbers, may have altered the soil microbial composition and that Captina silt loam can develop an effective degrader population under tested conditions. [ABSTRACT FROM AUTHOR]