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Microbial succession has been suggested to supplement established postmortem interval (PMI) estimation methods for human remains. Due to limitations of entomological and morphological PMI methods, microbes are an intriguing target for forensic applications as they are present at all stages of decomposition. Previous machine learning models from soil necrobiome data have produced PMI error rates from two and a half to six days; however, these models are built solely on amplicon sequencing of biomarkers (e.g., 16S, 18S rRNA genes) and do not consider environmental factors that influence the presence and abundance of microbial decomposers. This study builds upon current research by evaluating the inclusion of environmental data on microbial-based PMI estimates from decomposition soil samples. Random forest regression models were built to predict PMI using relative taxon abundances obtained from different biological markers (bacterial 16S, fungal ITS, 16S-ITS combined) and taxonomic levels (phylum, class, order, OTU), both with and without environmental predictors (ambient temperature, soil pH, soil conductivity, and enzyme activities) from 19 deceased human individuals that decomposed on the soil surface (Tennessee, USA). Model performance was evaluated by calculating the mean absolute error (MAE). MAE ranged from 804 to 997 accumulated degree hours (ADH) across all models. 16S models outperformed ITS models (p = 0.006), while combining 16S and ITS did not improve upon 16S models alone (p = 0.47). Inclusion of environmental data in PMI prediction models had varied effects on MAE depending on the biological marker and taxonomic level conserved. Specifically, inclusion of the measured environmental features reduced MAE for all ITS models, but improved 16S models at higher taxonomic levels (phylum and class). Overall, we demonstrated some level of predictability in soil microbial succession during human decomposition, however error rates were high when considering a moderate population of donors. [ABSTRACT FROM AUTHOR]

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products. [ABSTRACT FROM AUTHOR]

Viruses, with an estimated abundance of 1031 on Earth, are an important component of soil ecosystems. As obligate parasites that entirely depend on hosts for reproduction and survival, viruses have been linked to microbial community diversity and metabolic activities in soil. Emerging evidence indicates that soil viruses influence a broad-spectrum of processes that sustain soil biodiversity, biogeochemical cycling, fertility, and plant health. Research on soil viruses is in its early stages. Even observational assessments of viral ecology such as abundance, diversity, distribution, life strategies, ecological relevance, and functions, are only just beginning to be revealed. In this review, we summarize the state of knowledge concerning the potential function(s) of soil viruses and how they likely influence microbial community composition, nutrient cycles, and carbon dynamics for example. As major drivers of microbial mortality and functioning across a wide range of spatial and temporal scales, soil viruses appear to be key regulators of cellular metabolism and microbial community properties and as well as biogeochemical processes critical to ecosystem function. We conclude that soil viruses are an indispensable component of soil ecology demanding further investigation. Defining abiotic interactions of viruses within the soil environment, revealing the virus-host interaction networks, and elucidating the roles of soil viruses in carbon and nutrient cycling are but a few of the many aspects of soil viral ecology worthy of future investigation. A more complete view of viral participation in soil food webs in the face of a changing climate will lead to improved management of soil ecosystem services and environmental sustainability. [ABSTRACT FROM AUTHOR]

Biodegradable mulch films (BDMs) are a sustainable and promising alternative to non-biodegradable polyethylene mulches used in crop production systems. Nitrogen amendments in the form of fertilizers are used by growers to enhance soil and plant-available nutrients; however, there is limited research on how these additions impact the biodegradation of BDMs tilled into soils. A 4-month laboratory incubation study using soil microcosms was used to investigate the effects of inorganic (ammonium nitrate) and organic (urea and amino acids) nitrogen application on biodegradation of BDMs. We investigated the response of soil bacterial, fungal, and ammonia-oxidizing microbial abundance along with soil nitrogen pools and enzyme activities. Microcosms were comprised of soils from two diverse climates (Knoxville, TN, USA, and Mount Vernon, WA, USA) and BioAgri, a biodegradable mulch film made of Mater-Bi®, a bioplastic raw material containing starch and poly(butylene adipate-co-terephthalate) (PBAT). Both organic and inorganic nitrogen amendments inhibited mulch biodegradation, soil bacterial abundances, and enzyme activities. The greatest inhibition of mulch biodegradation in TN soils was observed with urea amendment where biodegradation was reduced by about 6 % compared to the no-nitrogen control. In WA soils, all nitrogen amendments suppressed biodegradation by about 1 % compared to the no-nitrogen control. Ammonia monooxygenase amoA gene abundances were increased in TN soils in all treatments but reduced for all treatments in WA soils. However, a significantly higher nitrate concentration and a lower ammonium concentration were seen for all nitrogen treatments compared to no-nitrogen controls in both TN and WA. This study suggests that the addition of nitrogen, particularly inorganic amendments, could slow down mulch biodegradation but that mulch biodegradation does not negatively affect soil nitrification activity. [ABSTRACT FROM AUTHOR]

Mammalian decomposition provides pulses of organic matter to the local ecosystem creating ephemeral hotspots of nutrient cycling. While changes to soil biogeochemistry in these hotspots have been described for C and N, patterns associated with deposition and cycling of other elements have not received the same attention. The goal of our study was to evaluate temporal changes to a broad suite of dissolved elements in soils impacted by human decomposition on the soil surface including: 1) abundant mineral elements in the human body (K, Na, S, P, Ca, and Mg), 2) trace elements in the human body (Fe, Mn, Se, Zn, Cu, Co, and B), and 3) Al which is transient in the human body but common in soils. We performed a four-month human decomposition trial at the University of Tennessee Anthropology Research Facility and quantified elemental concentrations dissolved in the soil solution, targeting the mobile and bioavailable fraction. We identified three groups of elements based on their temporal patterns. Group 1 elements appeared to be cadaver-derived (Na, K, P, S) and their persistence in soil varied based upon soluble organic forms (P), the dynamics of the soil exchange complex (Na, K), and gradual releases attributable to microbial degradation (S). Group 2 elements (Ca, Mg, Mn, Se, B) included three elements that have greater concentrations in soil than would be expected based on cadaver inputs alone, suggesting that these elements partially originate from the soil exchange (Ca, Mg), or are solubilized as a result of soil acidification (Mn). Group 3 elements (Fe, Cu, Zn, Co, Al) increased late in the decomposition process, suggesting a gradual solubilization from soil minerals under acidic pH conditions. This work presents a detailed longitudinal characterization of changes in dissolved soil elements during human decomposition furthering our understanding of elemental deposition and cycling in these environments. [ABSTRACT FROM AUTHOR]

Biodegradable mulch films (BDMs) are a sustainable and promising alternative to non-biodegradable polyethylene mulches used in crop production systems. Nitrogen amendments in the form of fertilizers are used by growers to enhance soil and plant-available nutrients, however, there is limited research on how these additions impact biodegradation of BDMs tilled into soils. A four-month soil microcosm study was used to investigate the effects of inorganic (ammonium nitrate) and organic (urea and amino acids) nitrogen application on biodegradable mulch decomposition. We investigated the response of soil bacterial, fungal and ammonia-oxidizing microbial abundance along with soil nitrogen pools and enzyme activities. Microcosms were comprised of soils from two diverse climates (Knoxville, TN, USA and Mount Vernon, WA, USA) and BioAgri, a biodegradable mulch film made of Mater-Bi®; a bioplastic raw material containing starch and poly(butylene adipate-co-terephthalate) (PBAT). Both organic and inorganic nitrogen amendments inhibited mulch decomposition, soil bacterial abundances and enzyme activities. The greatest inhibition of mulch biodegradation in TN soils was observed with urea amendment where biodegradation was reduced by about 6 % compared to the no-nitrogen control. In WA soils, all nitrogen amendments suppressed biodegradation by about 1 % compared to the no-nitrogen control. Ammonia monooxygenase amoA gene abundances were increased in TN soils in all treatments, but reduced for all treatments in WA soils. However, a significantly higher nitrate and lower ammonium concentration was seen for all nitrogen treatments compared to no-nitrogen controls in both TN and WA. This study suggests that addition of nitrogen, particularly inorganic amendments, could negatively affect mulch decomposition but that mulch decomposition does not negatively affect soil nitrification activity. [ABSTRACT FROM AUTHOR]

Soil microbial transformation of nitrogen (N) in nutrient-limited native C4 grasslands can be affected by N fertilization rate and C4 grass species. Here, we report in situ dynamics of the population size (gene copy abundances) and activity (transcript copy abundances) of five functional genes involved in soil N cycling (nifH, bacterial amoA, nirK, nirS, and nosZ) in a field experiment with two C4 grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) under three N fertilization rates (0, 67, and 202 kg N ha-1). Diazotroph (nifH) abundance and activity were not affected by N fertilization rate nor grass species. However, moderate and high N fertilization promoted population size and activity of ammonia oxidizing bacteria (AOB, quantified via amoA genes and transcripts) and nitrification potential. Moderate N fertilization increased abundances of nitrite-reducing bacterial genes (nirK and nirS) under switchgrass but decreased these genes under big bluestem. The activity of nitrous oxide reducing bacteria (nosZ transcripts) was also promoted by moderate N fertilization. In general, high N fertilization had a negative effect on N-cycling populations compared to moderate N addition. Compared to big bluestem, the soils planted with switchgrass had a greater population size of AOB and nitrite reducers. The significant interaction effects of sampling season, grass species, and N fertilization rate on N-cycling microbial community at genetic-level rather than transcriptional-level suggested the activity of N-cycling microbial communities may be driven by more complex environmental factors in native C4 grass systems, such as climatic and edaphic factors. [ABSTRACT FROM AUTHOR]