Soil Microbial Ecology Research Articles

Impacts of metallic nanoparticles and transformed products on soil health

Widespread usage of nanotechnology has increased the release of metallic nanoparticles (MNPs) into the environment, which are mostly engineered. Agricultural soil is one of the most important sinks for MNPs. While numerous studies have focused on understanding the phytotoxicity of MNPs, and the extent and pathways of their accumulation in plants, the impacts of MNPs on soil health are only gaining attention recently. A comprehensive review summarizing the interactions of MNPs with soil is yet available. This review aims to fill the gap by evaluating the impacts of common MNPs on soil properties. Specifically, we examined the effects of MNPs on soil physical properties, the availability of plant nutrients and heavy metals from the perspective of food safety and security, as well as soil microbial ecology and microbial community associated with nutrient and carbon cycling. We underscored the impacts of environmental transformation of MNPs on soil health. Compared with soil physical and chemical properties, biological parameters of soil health are more susceptible to the impact of MNPs. Overall, the effects of MNPs and their transformed products on soil health vary with soils, MNPs, and exposure duration and dosage.

Comparison of soil microbial community between planted woodland and natural grass vegetation on the Loess Plateau

Soil microorganisms play an important role in regulating subsurface ecological processes. Planted woodland and natural grass vegetation are the main vegetation restoration strategies for preventing soil erosion on the Loess Plateau of China. However, the response of soil microbial community and diversity to planted woodland and natural grass vegetation is largely unknown in this region. Here, we investigated soil microbial community and diversity using high-throughput sequencing approaches in planted woodland and natural grass vegetation. We found a disproportionate influence of planted woodland and natural grass vegetation on soil microbial diversity, and there was an increase of soil fungal diversity and a decrease of soil bacterial diversity in planted woodland. Both soil pH and soil organic carbon (SOC) were highly related to soil microbial diversity in planted woodland and natural grass vegetation. Moreover, we found the complex interaction networks of soil fungal community in planted woodland. Meanwhile, there were the higher total path coefficients of soil fungal diversity and the lower total path coefficients of bacterial diversity in planted woodland according to SEM (structural equation modeling). Besides, planted woodland explained more variation to soil fungal diversity and natural grass vegetation explained more variation to soil bacterial diversity, indicating that soil fungal diversity was more easily affected by planted woodland, while soil bacterial diversity was more easily affected by natural grass vegetation. To enhance the balance of soil microbial diversity, we suggested that both planted woodland and natural grass vegetation are needed in this region, highlighting the necessity of understanding soil microbial ecology to manage vegetation restoration on the Loess Plateau of China.

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated — the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or ‘extracellular polymeric substances’ (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R2 = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil’s structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS —as opposed to simply increasing the total SOC content— may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.

Influence of oats cover crop preceding dryland lucerne establishment on some aspects of soil microbial ecology

The use of cover crops to enhance soil ecology is widely propagated. Soil samples were collected at five depths from plots in newly established (four months) dryland lucerne (Medicago sativa) pasture. Preceding this establishment, the plots were either under Saia oats (Avena strigose) cover crop, or no cover crop (managed with herbicides). Variables studied were soil aggregate stability, active carbon (KMnO4 oxidation), Solvita® nitrogen and carbon, protozoa (Most Probable Number) and carbon utilisation (Biolog Ecoplates™). Principal component analysis (PCA) clearly showed associations between variables and the cover crop × depth treatments (two cover crop treatments – with and without cover crop), and five depth treatments (0–5, 5–10, 10–15, 15–20 and 20–30 cm). The PCA explained 72.9% of the total variation with the first three components (F1, F2 and F3). Protozoa separated clearly from the other variables. Discriminant analysis showed three distinct groups, namely 0–5 cm depth in both treatments, 5–10 cm depth with cover crop, while all others were in group 3. From these preliminary results it is clear that there are definitely differences in the effect of either a cover crop or no cover crop on some aspects of soil ecology.

Ecological Effects of Soil Microplastic Pollution

As a new type of environmental pollutant, microplastics pose a serious threat to soil ecosystems. We reviewed the classification and source of soil microplastics, separation, detection methods and existing problems. The pollution of soil microplastics and the adsorption effect and mechanism of microplastics on pollutants are summarized. The effects on soil animals, microbial ecology and carbon, nitrogen and other material cycles were analyzed. Furthermore, the ecological effects of microplastics are proposed, which provides new ideas for the study of soil microplastics in the future.

Relationship between the microbial community and catabolic diversity in response to conservation tillage

The present study investigates the microbial (bacterial and fungal) community diversity and carbon substrates utilization in rhizosphere and bulk soil under three tillage practices (chisel plow, zero, and plow tillage) by using high-throughput sequencing technology and community-level physiological profiles. Conservation tillage practices increased the DOC, SOC, and invertase activity in bulk soil compared with conventional tillage. Tillage disturbances changed the soil microbial phylogenetic composition and utilization abilities of carbon substrates, and there was a significant positive correlation between soil microbial alpha diversity and catabolic diversity under different tillage practices. The soil microbial phylogenetic composition was significantly different with different soil types (rhizosphere and bulk) under three tillage practices, which had great influence on carbon substrate utilization. The soil physicochemical parameters were significantly correlated with microbial taxonomy composition. Structural equation model (SEM) analysis suggested that the relative abundances of Proteobacteria (Alpha- and Betaproteobacteria), Bacteroidetes, Capnodiales, and Pleosporales in the rhizosphere helped in the utilization of amino acids, carbohydrates, and carboxylic acid under different tillage practices. Our results suggested that conservation tillage practices and crop root activities modified soil physicochemical parameters and enrich soil nutrient conditions, which contributes to differences of soil microbial phylogenetic and taxonomic compositions, thereby increasing copiotrophic microbial populations in the rhizosphere and enhances metabolic capacities. Thus, these results can improve our understanding of the roles of conservation tillage in changing soil microbial community and catabolic diversity, as well as can help to establish a profitable agroecosystem to enhance soil nutrient conditions and modify soil microbial ecology, in turn improving plant production sustainability.

Soil properties and microbial communities are the main contributors to aboveground vegetative biomass in reseeded grassland after long-term growth

The overall production of degraded grassland ecosystems can be improved by reseeding appropriate species, but the responses of soil microbes to reseeded grassland after a long-term growth, especially the mediation effects of soil chemical compounds on the soil microbial community composition, have rarely been reported. In this study, we reseeded a degraded grassland with Bromus inermis Leyss and investigated the changes in aboveground (grassland biomass) and belowground factors (soil properties, soil chemical compounds, soil microbial diversity, and community) under reseeded and non-reseeded treatments. The reseeding of B. inermis significantly (P < 0.05) enchacecd the aboveground vegetative biomass by 22.72% as compared with the plots that were not reseeded. Significant (P < 0.05) differences were also observed in the soil chemical compounds and microbial diversity and community between the reseeded and non-reseeded treatments. Soil bacterial (R2 = 0.6271, P = 0.0007) and fungal α-diversity (R2 = 0.5895, P = 0.0013) were both positively correlated with grassland biomass. Moreover, the community compositons of soil bacterial (R = 0.465, P = 0.002) and fungal (R = 0.720, P = 0.001) also had significant correlations with grassland biomass. Actinoplanes, Streptomyces, Bacillus, and Mesorhizobium were identified as potential agents for promoting grassland growth. Network analysis showed that the assemblages of soil microbes in the reseeding treatment formed larger and more complex networks than those in the non-reseeding treatment. Our study, cutting in terms of soil microbial ecology, provides a valuable model for explaining the aboveground responses to the establishment of perennial grass species in degraded grasslands.

The Variation of the Soil Bacterial and Fungal Community Is Linked to Land Use Types in Northeast China

From the west to the east across Northeast China, there are three major land use types, ranging from agricultural-pastoral interlaced land, crop land, and forest land. The soil microbial community of each land use type has been reported; however, a thorough comparison of the soil microbial ecology of soils from each land use type has not been made. In the current study, soil samples from agricultural-pastoral land, crop land, and an artificial economic forest were collected from Tongliao, Siping, and Yanji, respectively. The structure and composition of bacterial and fungal communities was investigated by a next generation sequencing protocol, and soil physicochemical properties were also determined. Pair-wise analysis showed some soil parameters were significantly different between agricultural-pastoral land and crop land or forest land, while those soil parameters shared more similarities in crop land and forest land soils. Principal coordinates analysis and dissimilarity analyses jointly indicated that bacterial and fungal communities from each sampling site were quite different. Canonical correspondence analysis and a partial Mantel test showed that the community structures of bacteria and fungi were mainly affected by clay, pH, water soluble organic carbon (WSOC), and total soluble nitrogen (TN). Co-occurrence network analysis and the associated topological features revealed that the network of the bacterial community was more complex than that of the fungal community. Clay, pH, WSOC, and NH4+-N were major drivers and pH and WSOC were major factors in shaping the network of the bacterial community and the fungal community, respectively. In brief, our results indicated that microbial diversity, co-occurrence network patterns, and their shaping factors differed greatly among soils of distinct land use types in Northeast China. Our data also provided insights into the sustainable use of soils under different land use types.

Selection, Succession, and Stabilization of Soil Microbial Consortia.

Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest.

Drylands occupy approximately 41% of the Earth’s terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria (‘Candidatus Solibacter’ and ‘Candidatus Koribacter’) in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.

Consistent spatial distribution patterns of bacterial communities revealed by serial time-archived soils from long-term field experiments

Many precious air-dried soil samples are currently stored by institutions across the world, and they have been proved useful in retrieving historical information of soil microbial ecology, such as the shifts of microbial populations and the effects of agricultural managements on soil microbial communities. However, most of those retrospective studies on microorganisms in archived soils were mainly conducted through PCR-DGGE or T-RFLP analysis, which was less sensitive to low-abundance species. In order to assess whether archived soils could reveal the spatial distribution of microbial communities at large spatial scale, especially the rare microbial taxa, a total of 117 serial time-historical samples from eight long-term field experimental stations of the Chinese Ecosystem Research Network were analyzed using high-throughput sequencing. The non-metric multidimensional scaling (NMDS) analyses showed that both the total bacterial communities and the rare bacterial subcommunities were distinctly clustered into different groups corresponding to each experimental station, and that analogous distribution patterns of bacterial communities existed between each two sampling years for both the total and the rare taxa, though the microbial community composition changed over time. The corresponding hierarchical clustering analyses demonstrated that soil bacterial communities for both the total and the rare taxa could be clustered into five groups for all samples and for the sub-samples of each sampling year, which corresponded to five eco-geographic regions in the Eco-Geographic Regional System of China. The results from this investigation highlighted the great value of serial time-archived soils in revealing the spatial distribution patterns of bacterial communities for both the total and the rare taxa at large spatial scale.

The known and the unknown in soil microbial ecology.

The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.

Trichoderma-Inoculation and Mowing Synergistically Altered Soil Available Nutrients, Rhizosphere Chemical Compounds and Soil Microbial Community, Potentially Driving Alfalfa Growth

Trichoderma spp. are proposed as major plant growth-promoting fungi (PGPF) to increase plants growth and productivity. Mowing can stimulate aboveground regrowth to improve plant biomass and nutritional quality. However, the synergistic effects of Trichoderma and mowing on plants growth, particularly the underlying microbial mechanisms mediated by rhizosphere soil chemical compounds, have rarely been reported. In the present study, we employed Trichoderma harzianum T-63 and conducted a pot experiment to investigate the synergistic effect of Trichoderma-inoculation and mowing on alfalfa growth, and the potential soil microbial ecological mechanisms were also explored. Alfalfa treated with Trichoderma-inoculation and/or mowing (T, M, and TM) had significant (P < 0.05) increases in plant shoot and root dry weights and soil available nutrients (N, P, and K), compared with those of the control (CK). Non-metric multidimensional scaling (NMDS) demonstrated that the rhizosphere chemical compounds and soil bacterial and fungal communities were, respectively, separated according to different treatments. There was a clear significant (P < 0.05) positive correlation between alfalfa biomass and the relative abundance of Trichoderma (R2 = 0.3451, P = 0.045). However, Pseudomonas, Flavobacterium, Arthrobacter, Bacillus, Agrobacterium, and Actinoplanes were not significantly correlated with alfalfa biomass. According to structure equation modeling (SEM), Trichoderma abundance and available P served as primary contributors to alfalfa growth promotion. Additionally, Trichoderma-inoculation and mowing altered rhizosphere soil chemical compounds to drive the soil microbial community, indirectly influencing alfalfa growth. Our research provides a basis for promoting alfalfa growth from a soil microbial ecology perspective and may provide a scientific foundation for guiding the farming of alfalfa.

Influence of biochar application on growth of Oryza sativa and its associated soil microbial ecology

In this study, biochar was produced from three biomass feedstocks such as fruits of Cassia fistula and Caesalpinia sp. and barks of Eucalyptus globulus. The samples of the obtained biochar were characterized for pH, physiochemical properties, surface morphology, and surface functional groups. The obtained biochar samples were further studied with/without the combination of urea for their plant growth enhancement properties including the germination studies and effect on shoot and root growth of rice plants. Biochar produced from C. fistula fruits at 1.5% concentration increased the plant shoot height 18% higher than the control plants. Eucalyptus sp. barks’ biochar application at 0.5% concentration also increased the plant shoot height 12% longer than the control. However, the biochar produced from Caesalpinia sp. did not increase the shoot length. Yet, a generalized increase in root length was observed with the application of biochar. The combined application of nitrogen fertilizer (urea) and biochar together reverted the effect of biochar on the shoot length increase. Phospholipid-derived fatty acid (PLFA) characterization of soil revealed that soil biota shifts when soil was supplemented with the biochar. The bacterial community increased and a loss of fungal community was observed with the application of biochar.

Microfluidic qPCR Enables High Throughput Quantification of Microbial Functional Genes but Requires Strict Curation of Primers

Quantification of microbial functional genes enhances predictions of soil biogeochemical process rates, but reliance on low-throughput quantitative PCR (qPCR) limits the scope of ecological studies to a handful of targets. Here, we explore whether microfluidic qPCR (MFQPCR) is a viable high-throughput alternative for functional gene quantification, by evaluating the efficiency, specificity and sensitivity of 29 established and 12 newly designed primer pairs targeting taxonomic, nitrogen-cycling and hydrocarbon degradation genes in gDNA soil extracts, under three different sets of MFQPCR assay conditions. Without curation, commonly-used qPCR primer pairs yielded an extreme range of reaction efficiencies (25.9% - 100.1%), but when conditions were optimized, MFQPCR produced copy-number estimates comparable to traditional qPCR. To guide microbial soil ecologists considering adoption of MFQPCR, we present suggestions for primer selection, including omission of inosines, degeneracy scores of < 9, amplicon sizes of ≤ 211 bp, and GC content of 32-61%. We conclude that, while the nanoliter reaction volumes, rapid thermocycling and one-size-fits-all reaction conditions of MFQPCR necessitates more stringent primer selection criteria than is commonly applied in soil microbial ecology, the ability to quantify up to 96 targets in 96 samples makes MFQPCR a valuable tool for monitoring shifts in functional community abundances. MFQPCR will particularly suit studies targeting multiple clade-specific functional genes, or when primer design is informed by previous knowledge of the environment.

The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil.

The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.

Assessing New Developments in IRIS Technology

Reducing soil conditions may impact more static properties like soil morphology, as well as more dynamic soil chemical properties and microbial ecology. Identifying reducing conditions is especially important when evaluating wetland soil systems. Indicator of Reduction in Soils (IRIS) tubes have been approved by the National Technical Committee for Hydric Soils (NTCHS) as a method to identify reducing soil conditions. Recently, a new development in IRIS technology utilizing flexible films has emerged. IRIS films are strips of vinyl sheeting painted with iron- or manganeseoxide paint. The films are intended to simplify field work and facilitate acquisition and computer analysis of IRIS images. This mesocosm study demonstrates that IRIS films perform comparably to IRIS tubes and accurately document reducing soil conditions.

A horizontal permeable reactive barrier stimulates nitrate removal and shifts microbial ecology during rapid infiltration for managed recharge

We present results from field experiments linking hydrology, geochemistry, and microbiology during infiltration at a field site that is used for managed aquifer recharge (MAR). These experiments measured how a horizontal permeable reactive barrier (PRB) made of woodchips impacted subsurface nitrate removal and microbial ecology. Concentrations of dissolved organic carbon consistently increased in infiltrating water below the PRB, but not in un-amended native soil. The average nitrate removal rate in soils below the PRB was 1.5 g/m2/day NO3-N, despite rapid infiltration (up to 1.9 m/d) and a short fluid residence time within the woodchips (≤6 h). In contrast, 0.09 g/m2/day NO3-N was removed on average in native soil. Residual nitrate in infiltrating water below the PRB was enriched in δ15N and δ18O, with low and variable isotopic enrichment factors that are consistent with denitrification during rapid infiltration. Many putative denitrifying bacteria were significantly enhanced in the soil below a PRB; Methylotenera mobilis and genera Microbacterium, Polaromonas, and Novosphingobium had log2 fold-changes of +4.9, +5.6, +7.2, and +11.8, respectively. These bacteria were present before infiltration and were not enhanced in native soil. It appears that the woodchip PRB contributed to favorable conditions in the underlying soil for enhanced nitrate removal, quantitatively shifting soil microbial ecology. These results suggest that using a horizontal PRB could improve water quality during rapid infiltration for MAR.

Alpine soil microbial ecology in a changing world.

Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.

Foodborne pathogens in horticultural production systems: Ecology and mitigation

Foodborne pathogen outbreaks have become an increasing problem in the horticultural industry due to changes in diets, production, processing and distribution practices, as well as greater awareness and detection. Once produce is infected, outbreaks can spread rapidly resulting in illness and even death among large groups of people. Strict new food safety laws have been implemented to reduce risks, but outbreaks are still occurring. Pathogens with the greatest threat in ready-to-eat horticultural crops include Salmonella enterica, Escherichia coli (STEC), and Listeria monocytogenes, with contamination introduced through animal manure, water, seeds and plant debris. While previously thought to be only transient inhabitants of horticultural production systems, it is now clear that enteric pathogens are adapted to survive for prolonged periods outside of their animal hosts, attaching tenaciously to plants via biofilm formation and internalization in plant tissues. Management practices including treating animal manure, water and seeds, increasing soil biological diversity and activity, and limiting damage to plants via pests and equipment can help reduce food safety risks in pre-harvest production systems. Further reducing food safety risks in these systems will require innovative, interdisciplinary research that integrate the fields of soil microbial ecology, plant pathology, plant breeding and engineering. Specifically, we advocate for additional research to: 1) better understand how soil and phyllosphere ecology affects pathogen residence time, 2) identify key traits and markers to integrate selection for enteric pathogens into crop breeding programs, and 3) develop new detection technologies that rapidly and accurately detect enteric pathogens on produce.