Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Improved SARS-CoV-2 RNA recovery in wastewater matrices using a CTAB-based extraction method

Wastewater-based epidemiology has allowed tracking the magnitude and distribution of SARS-CoV-2 in communities, allowing public health officials to prepare for impending outbreaks. While many factors influence recovery of SARS-CoV-2 from wastewater, proper extraction, concentration, and purification of RNA are key steps to ensure accurate detection of viral particles. The aim of this study was to compare the efficiency of four commonly used RNA extraction methods for detection of the SARS-CoV-2 RNA genome in sewage samples artificially inoculated with the virus, in order to identify a protocol that improves viral recovery. These methods included CTAB-based, TRIzol-based, and guanidinium thiocyanate (GTC)-based extraction procedures coupled with silica spin column-based purification, and an automated extraction/purification protocol using paramagnetic particles. Following RNA extraction, virus recovery rates were compared using RT-qPCR-based detection. The CTAB-based approach yielded the highest recovery rates and was the only method to consistently demonstrate stable virus recovery percentages regardless of the specific physicochemical characteristics of the samples tested. The TRIzol method proved to be the second most effective, yielding significantly higher recovery rates compared to both the GTC-based and the automated extraction methods. These results suggest that the CTAB-based approach could be a useful tool for the recovery of viral RNA from complex wastewater matrices.

Molecular docking and metagenomics assisted mitigation of microplastic pollution

Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.

A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory

The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.

Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert

The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.

Prior exposure of microbial communities to seawater reduces resilience but increases compositional and functional resistance to flooding events

Storm surges, flooding, and the encroachment of seawater onto agricultural land are predicted to increase with climate change. These flooding events fundamentally alter many soil properties and have knock-on effects on the microbial community composition and its functioning. The hypotheses tested in this study were (1) that the extent of change (resistance) of microbial community functioning and structure during seawater flooding is a factor of pre-adaptation to the stress, and (2) if structure and function are altered, the pre-adaptation will result in communities returning to previous state prior to flooding (resilience) faster than unexposed communities. We chose a naturally occurring saltmarsh-terrestrial pasture gradient from which three elevations were selected to create mesocosms. By selecting these sites, we were able to incorporate the legacy of differing levels of seawater ingress and exposure. Mesocosms were submerged in seawater for 0, 1, 96- and 192-h, with half of the mesocosms sacrificed immediately after flooding, and the other half taken after a 14 day "recovery" period. The following parameters were monitored: 1) changes in soil environmental parameters, 2) prokaryotic community composition, and 3) microbial functioning. Our results indicated that any length of seawater inundation significantly altered the physicochemical properties of all the soils, although a greater change is observed in the pasture site compared to the saltmarsh sites. These changes remained following a recovery period. Interestingly, our results indicated that for community composition, there was a high degree of resistance for the Saltmarsh mesocosms, with the Pasture mesocosm displaying higher resilience. Further, we observed a functional shift in the enzyme activities with labile hemicellulose being preferentially utilised over cellulose, with the effect increasing with longer floods. These results suggest that changing bacterial physiology is more critical to understanding the impact of storm surges on agricultural systems than bulk community change.

Evaluation and Assessment of Trivalent and Hexavalent Chromium on Avena sativa and Soil Enzymes

Chromium (Cr) can exist in several oxidation states, but the two most stable forms-Cr(III) and Cr(VI)-have completely different biochemical characteristics. The aim of the present study was to evaluate how soil contamination with Cr(III) and Cr(VI) in the presence of Na2EDTA affects Avena sativa L. biomass; assess the remediation capacity of Avena sativa L. based on its tolerance index, translocation factor, and chromium accumulation; and investigate how these chromium species affect the soil enzyme activity and physicochemical properties of soil. This study consisted of a pot experiment divided into two groups: non-amended and amended with Na2EDTA. The Cr(III)- and Cr(VI)-contaminated soil samples were prepared in doses of 0, 5, 10, 20, and 40 mg Cr kg-1 d.m. soil. The negative effect of chromium manifested as a decreased biomass of Avena sativa L. (aboveground parts and roots). Cr(VI) proved to be more toxic than Cr(III). The tolerance indices (TI) showed that Avena sativa L. tolerates Cr(III) contamination better than Cr(VI) contamination. The translocation values for Cr(III) were much lower than for Cr(VI). Avena sativa L. proved to be of little use for the phytoextraction of chromium from soil. Dehydrogenases were the enzymes which were the most sensitive to soil contamination with Cr(III) and Cr(VI). Conversely, the catalase level was observed to be the least sensitive. Na2EDTA exacerbated the negative effects of Cr(III) and Cr(VI) on the growth and development of Avena sativa L. and soil enzyme activity.

An improved method for intracellular DNA (iDNA) recovery from terrestrial environments

The simultaneous extraction of intracellular DNA (iDNA) and extracellular DNA (eDNA) can help to separate the living in situ community (represented by iDNA) from background DNA that originated both from past communities and from allochthonous sources. As iDNA and eDNA extraction protocols require separating cells from the sample matrix, their DNA yields are generally lower than direct methods that lyse the cells within the sample matrix. We, therefore, tested different buffers with and without adding a detergent mix (DM) in the extraction protocol to improve the recovery of iDNA from surface and subsurface samples that covered a variety of terrestrial environments. The combination of a highly concentrated sodium phosphate buffer plus DM significantly improved iDNA recovery for almost all tested samples. Additionally, the combination of sodium phosphate and EDTA improved iDNA recovery in most of the samples and even allowed the successful extraction of iDNA from extremely low-biomass iron-bearing rock samples taken from the deep biosphere. Based on our results, we recommend using a protocol with sodium phosphate in combination with either a DM (NaP 300 mM + DM) or EDTA (NaP + EDTA 300 mM). Furthermore, for studies that rely on the eDNA pool, we recommend using buffers solely based on sodium phosphate because the addition of EDTA or a DM resulted in a decrease in eDNA for most of the tested samples. These improvements can help reduce community bias in environmental studies and contribute to better characterizations of both modern and past ecosystems.

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.

Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics

Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.

Effects of Bradyrhizobium Co-Inoculated with Bacillus and Paenibacillus on the Structure and Functional Genes of Soybean Rhizobacteria Community

Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two PGPR strains, Bacillus aryabhattai MB35-5 (BA) and Paenibacillus mucilaginosus 3016 (PM), alone or in different combinations on the soil properties and rhizosphere bacterial community composition of soybean (Glycine max). Additionally, metagenomic sequencing was performed to elucidate the profile of functional genes. Inoculation with compound microbial inoculant containing R5038 and BA (RB) significantly improved nodule nitrogenase activity and increased soil nitrogen content, and urease activity increased the abundance of the nitrogen cycle genes and Betaproteobacteria and Chitinophagia in the rhizosphere. In the treatment of inoculant-containing R5038 and PM (RP), significant changes were found for the abundance of Deltaproteobacteria and Gemmatimonadetes and the phosphorus cycle genes, and soil available phosphorus and phosphatase activity were increased. The RBP inoculants composed of three strains (R5038, BA and PM) significantly affected soybean biomass and the N and P contents of the rhizosphere. Compared with RB and RP, RBP consistently increased soybean nitrogen content, and dry weight. Overall, these results showed that several PGPR with different functions could be combined into composite bacterial inoculants, which coordinately modulate the rhizosphere microbial community structure and improve soybean growth.

The PortaLyzer, a DIY tool that allows environmental DNA extraction in the field

The PortaLyzer is a portable homemade device that allows researchers to perform bead-beating steps commonly found in environmental DNA (eDNA) extraction protocols in the field without access to power. This allows researchers to preserve in situ organism abundance by beginning eDNA extraction quickly. The PortaLyzer is composed of a variable speed, battery-powered multi-tool and a vortexer adapter plate. We used the PortaLyzer, in conjunction with the Qiagen DNEasy PowerSoil Pro kit, to successfully field process samples taken from the forelands of the Sólheimajökull and Kvíárjökull glaciers in Iceland, as well as soil samples acquired from a prairie in Indiana. Additionally, we provide evidence that samples held in Buffer CD2 of the DNEasy PowerSoil Pro Kit may be transported to traditional lab spaces and processed up to one month after the initial protocol steps, and still provide an equivalent DNA quality and abundance yield as those processed the same day. These improvements to DNA extraction protocols give researchers more flexibility while sampling, shipping and processing eDNA samples.

Amelioration of Organic Carbon and Physical Health of Structurally Disturbed Soil through Microbe–Manure Amalgam

Less precipitation, high temperature, and minimal natural vegetation are characteristic of regions having an arid climate. The harsh environment massively destructs the soil structure of that area by burning soil organic carbon, leading to deteriorated soil nutritional quality, creating a significant threat to agricultural production and food security. Direct application of organic wastes not only substitutes lost organic carbon but also restores soil structure and fertility. This study was conducted to assess the impact of organic amendments, i.e., farm manure (FM), poultry manure (PM), molasses (MO), and Exo-Poly Saccharides (EPS) producing rhizobacterial strains i.e., M2, M19, M22 amalgams as treatments. To assess the impact of treatments on soil carbon and structure restoration to hold more water and nutrients, a 42-day incubation experiment using a completely randomized design (CRD) under the two-factor factorial arrangement was conducted. Macro aggregation (0.25 to >1 mm), carbon retention in macro aggregates, active carbon (dissolved organic carbon, a mineral-associated organic carbon, microbial biomass carbon), total organic carbon, the carbon mineralization activities, and water retention capacities were observed to be highest in soils that were treated with (FM + M2, FM + M22, PM + M19, and MO + M19). Finally, we conclude that organics mineralization by microbial actions releases organic glues that not only impart particle aggregation but also conserve organics as aggregate entrapped carbon. Amalgamated application of microbe–manure combinations directly impacts soil structure and organic carbon contents, but in an indirect scenario, it improves the fertility and productivity of the soil. Therefore, it is strongly recommended to use organic manures and microbes in combination to restore structurally degraded lands.

Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes

Soil CH₄ fluxes are driven by CH₄-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH₄-cycling microbiomes to net surface CH₄ fluxes throughout a year in two grassland soils. CH₄ fluxes were highly dynamic: both soils were net CH₄ sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH₄ fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH₄ sinks. CH₄ uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH₄ emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH₄ sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH₄-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.

Exploitation of Plant Growth Promoting Bacteria for Sustainable Agriculture: Hierarchical Approach to Link Laboratory and Field Experiments

To feed a world population, which will reach 9.7 billion in 2050, agricultural production will have to increase by 35–56%. Therefore, more food is urgently needed. Yield improvements for any given crop would require adequate fertilizer, water, and plant protection from pests and disease, but their further abuse will be economically disadvantageous and will have a negative impact on the environment. Using even more agricultural inputs is simply not possible, and the availability of arable land will be increasingly reduced due to climate changes. To improve agricultural production without further consumption of natural resources, farmers have a powerful ally: the beneficial microorganisms inhabiting the rhizosphere. However, to fully exploit the benefits of these microorganisms and therefore to widely market microbial-based products, there are still gaps that need to be filled, and here we will describe some critical issues that should be better addressed.

Metagenomics: A New Direction in Ecology

Abstract

The prospects for application of metagenomic technologies in environmental studies are discussed. The advantages in investigating the taxonomic composition of aquatic and terrestrial ecosystems, as well as examples of trophic and phoric relationships found in ecosystems using the metagenomic approach, are described. The capabilities of metagenomics to study prokaryotic communities in complicated environments such as soils or animal intestines are shown. The role of relic DNA in the metagenome and the possibilities to study ancient organisms are highlighted. Particular attention is paid to the criticism of metagenomic technologies related to the low reproducibility of the sequencing data. Common methodological mistakes in bioinformatics processing of metagenomic data leading to misleading results are considered.

Ecotoxicity of herbicide carfentrazone-ethyl towards earthworm Eisenia fetida in soil

Herbicides pose a potential threat to the soil biodiversity and health. Carfentrazone-ethyl (CE), a triazolinones herbicide, is increasingly used in agricultural production. Its non-target toxic effects on soil microorganisms and soil enzymes are reported recently. However, the sublethal toxicity of CE on soil invertebrates like earthworms is not yet known. Therefore, in this work, the sublethal toxic effects of CE (0.05, 0.5, and 5.0 μg/g in soil) on the soil earthworm (Eisenia fetida) were evaluated using a battery of biomarkers including reactive oxygen species (ROS), enzyme (superoxide dismutase-SOD, catalase-CAT, peroxidase-POD, and glutathione S-transferase-GST) activities, malondialdehyde (MDA) contents, histopathological and DNA damage. Results indicated that CE increased ROS contents, enzyme activities, and MDA contents in the short-time (14 d), thus, causing a slight oxidative stress to E. fetida. However, the toxic effects of CE on earthworms gradually disappeared after 14 days. The CE did not cause histopathological and DNA damage in earthworms. Integrated Biological Response index (IBR) indicated that both concentration and exposure time of CE regulated its sublethal toxicity on earthworms. In conclusion, herbicide CE is safe to soil invertebrate earthworms when applied at the recommended doses. Our results contribute to the current understanding of CE effects on soil earthworms, and can be useful in developing soil health strategies under agrochemical use.

Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery

Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.

KOMB: K-core based de novo characterization of copy number variation in microbiomes

Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response to perturbations. We describe KOMB, a novel method for tracking genome level dynamics within microbiomes. KOMB utilizes K-core decomposition to identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV) within microbiomes. K-core decomposition partitions the graph into shells containing nodes of induced degree at least K, yielding reduced computational complexity compared to prior approaches. Through validation on a synthetic community, we show that KOMB recovers and profiles repetitive genomic regions in the sample. KOMB is shown to identify functionally-important regions in Human Microbiome Project datasets, and was used to analyze longitudinal data and identify keystone taxa in Fecal Microbiota Transplantation (FMT) samples. In summary, KOMB represents a novel graph-based, taxonomy-oblivious, and reference-free approach for tracking CNV within microbiomes. KOMB is open source and available for download at https://gitlab.com/treangenlab/komb.

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.

The Threat of Pests and Pathogens and the Potential for Biological Control in Forest Ecosystems

Forests are an essential component of the natural environment, as they support biodiversity, sequester carbon, and play a crucial role in biogeochemical cycles—in addition to producing organic matter that is necessary for the function of terrestrial organisms. Forests today are subject to threats ranging from natural occurrences, such as lightning-ignited fires, storms, and some forms of pollution, to those caused by human beings, such as land-use conversion (deforestation or intensive agriculture). In recent years, threats from pests and pathogens, particularly non-native species, have intensified in forests. The damage, decline, and mortality caused by insects, fungi, pathogens, and combinations of pests can lead to sizable ecological, economic, and social losses. To combat forest pests and pathogens, biocontrol may be an effective alternative to chemical pesticides and fertilizers. This review of forest pests and potential adversaries in the natural world highlights microbial inoculants, as well as research efforts to further develop biological control agents against forest pests and pathogens. Recent studies have shown promising results for the application of microbial inoculants as preventive measures. Other studies suggest that these species have potential as fertilizers.

Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking

Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g., adhesion of DNA to the sample matrix, inefficient precipitation of DNA, pipetting errors and (partial) loss of the DNA pellet during DNA isolation), quality control is essential at all processing levels. In soil microbiology, particular attention has been paid to the inorganic component of the sample matrix affecting DNA extractability. In water quality testing, however, this aspect has mostly been neglected so far, although it is conceivable that these mechanisms have a similar impact. The present study was therefore dedicated to investigate possible matrix effects on results of water quality analysis. Field testing in an aquatic environment with pronounced chemo-physical gradients [total suspended solids (TSS), inorganic turbidity, total organic carbon (TOC), and conductivity] indicated a negative association between DNA extractability (using a standard phenol/chloroform extraction procedure) and turbidity (spearman ρ = −0.72, p < 0.001, n = 21). Further detailed laboratory experiments on sediment suspensions confirmed the hypothesis of inorganic turbidity being the main driver for reduced DNA extractability. The observed effects, as known from soil samples, were also indicated to result from competitive effects for free charges on clay minerals, leading to adsorption of DNA to these inorganic particles. A protocol modification by supplementing the extraction buffer with salmon sperm DNA, to coat charged surfaces prior to cell lysis, was then applied on environmental water samples and compared to the standard protocol. At sites characterized by high inorganic turbidity, DNA extractability was significantly improved or made possible in the first place by applying the adapted protocol. This became apparent from intestinal enterococci and microbial source tracking (MST)-marker levels measured by quantitative polymerase chain reaction (qPCR) (100 to 10,000-fold median increase in target concentrations). The present study emphasizes the need to consider inorganic turbidity as a potential loss factor in DNA extraction from water-matrices. Negligence of these effects can lead to a massive bias, by up to several orders of magnitude, in the results of molecular MST and fecal pollution diagnostics.

New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods

Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8–3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3–4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.

Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil

Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Continental-scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia

BACKGROUND AND AIMS

Mycorrhizal fungi are a critical component of the ecological niche of most plants and can potentially constrain their geographical range. Unlike other types of mycorrhizal fungi, the distributions of orchid mycorrhizal fungi (OMF) at large spatial scales are not well understood. Here, we investigate the distribution and diversity of Ceratobasidium OMF in orchids and soils across the Australian continent.

METHODS

We sampled 217 Ceratobasidium isolates from 111 orchid species across southern Australia and combined these with 311 Ceratobasidium sequences from GenBank. To estimate the taxonomic diversity of Ceratobasidium associating with orchids, phylogenetic analysis of the ITS sequence locus was undertaken. Sequence data from the continent-wide Australian Microbiome Initiative were used to determine the geographical range of operational taxonomic units (OTUs) detected in orchids, with the distribution and climatic correlates of the two most frequently detected OTUs modelled using MaxEnt.

KEY RESULTS

We identified 23 Ceratobasidium OTUs associating with Australian orchids, primarily from the orchid genera Pterostylis, Prasophyllum, Rhizanthella and Sarcochilus. OTUs isolated from orchids were closely related to, but distinct from, known pathogenic fungi. Data from soils and orchids revealed that ten of these OTUs occur on both east and west sides of the continent, while 13 OTUs were recorded at three locations or fewer. MaxEnt models suggested that the distributions of two widespread OTUs are correlated with temperature and soil moisture of the wettest quarter and far exceeded the distributions of their host orchid species.

CONCLUSIONS

Ceratobasidium OMF with cross-continental distributions are common in Australian soils and frequently have geographical ranges that exceed that of their host orchid species, suggesting these fungi are not limiting the distributions of their host orchids at large spatial scales. Most OTUs were distributed within southern Australia, although several OTUs had distributions extending into central and northern parts of the continent, illustrating their tolerance of an extraordinarily wide range of environmental conditions.

The Response of the Soil Microbiome to Contamination with Cadmium, Cobalt and Nickel in Soil Sown with Brassica napus

Soil fertility is determined by biological diversity at all levels of life, from genes to entire biocenoses. The aim of this study was to evaluate bacterial diversity in soil contaminated with Cd2+, Co2+ and Ni2+ and sown with Brassica napus. This is an important consideration because soil-dwelling microorganisms support phytoremediation and minimize the adverse effects of heavy metals on the environment. Microbial counts, the influence (IFHM) of Cd2+, Co2+ and Ni2+ on microorganisms, the colony development (CD) index, the ecophysiological diversity (EP) index and genetic diversity of bacteria were determined under controlled conditions. Soil contamination with Cd2+, Co2+ and Ni2+ significantly influenced microbial diversity and increased the values of CD and EP indices. The tested heavy metals decreased the genetic diversity of bacteria, in particular in the phyla Actinobacteria and Proteobacteria. Bacteria of the genera Arthrobacter, Devosia, Kaistobacter, Paenibacillus, Phycicoccus, Rhodoplanes and Thermomonas were identified in both contaminated and non-contaminated soil. These bacteria are highly resistant to soil contamination with Cd2+, Co2+ and Ni2+.

Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept

Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm³ densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.

Garlic (Allium sativum) based interplanting alters the heavy metals absorption and bacterial diversity in neighboring plants

Heavy metals are naturally occurring elements that have a high atomic weight and let out in the environment by agriculture, industry, mining and therapeutic expertise and thrilling amassing of these elements pollutes the environment. In this study we have investigated the potential of garlic interplanting in promoting hyper accumulation and absorption of heavy metals to provide a basis for phytoremediation of polluted land. Monoculture and inter-plantation of garlic were conducted to investigate the absorption of cadmium and lead contamination in the land. A group of experiments with single planting (monoculture) of Lolium perenne, Conyza canadensis and Pteris vittata as accumulators were used. The results have shown that garlic has a potential as a hyper accumulate and absorb heavy metals. It was found that the accumulation of Cd and Pb was much higher with inter-planting. Garlic boosts up the absorption of heavy metals in Lolium perenne of Cd 66% and Pb 44% respectively. The Inter-planting of garlic with Pteris vittata promotes the Cd 26% and Pb 15%. While the maximum accumulation of Lead 87% and Cadmium 77% occurred in Conyza canadensis herb plant. The bacterial diversity in the soil was analyzed for each experimental soil and was found that the Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, and Planctomycetes were commonly abundant in both single planting (monoculture) of ryegrass and interplanting ryegrass with garlic habitats. Variances were observed in the bacterial floral composition of single (monoculture) and intercropping (interplant) soils. Relative abundance of bacterial taxa revealed that the proportion of Proteobacteria, Acidobacteria, and Actinobacteria in the inter-planting group was slightly higher, while Firmicutes and Planctomycetes were low. This study provides the evidence to control the heavy metals contaminated soils with weed species. Growth promotion and heavy metal uptake of neighboring plants proved the specific plant-plant and plant-microbial associations with garlic plants. This inter-planting strategy can be used to improve heavy metal absorption.

The insufficient extraction of DNA from swine manures may underestimate the abundance of antibiotic resistance genes as well as ignore their potential hosts

Swine manure is considered as an extensive reservoir of antibiotic resistance genes (ARGs) spreading in the natural environment after application in soils. To understand whether ARGs abundance in swine manure is underestimated and the hosts are ignored, this study successively extracted DNA from swine manure six times and determined the abundance of several ARGs, class I integron (intI1), and 16S rRNA as well as the microbial communities. It is found that successive six DNA extraction of swine manures elevated the yield of DNA and strongly increased the abundance of ARGs, intI1, and 16S rRNA. Compared with single DNA extraction, the most dominant bacterial phylum in swine manures shifted from Proteobacteria to Firmicutes, and the dominant bacterial genera changed from Acinetobacter Clostridium after six DNA extraction. The ignored abundance of bacterial phylum and genus emphasized the possible hosts carrying these genes should be paid more attention. It is suggested that the successive DNA extraction of manures is required in the future study to improve the knowledge of estimating the risk and hosts of ARGs in manures entering the environment.

Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

Sequencing PCR‐amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen‐depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co‐occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

Comparison of performance and efficiency of four methods to extract genomic DNA from oil contaminated soils in southwestern of Iran

The wide spectrum of oil industry activities caused soil contaminants, as environmental concern in many areas of the world. Bioremediation of oily soils, as biological approach done by bacteria and fungi, is very important to eliminate this pollution. In this study four different metagenomic protocols for DNA extraction has been tested in order to sequence and identify the native bacterial species involved in remediation of oily soils. In this regard, 3 manual methods and a soil DNA extraction kit are used. In manual protocol, physical processes including the addition of silica beads and freezing samples by liquid nitrogen, chemical methods such as treating the lysozyme, and lysis buffer and proteinase K as biochemical methods were utilized for optimal extraction. Quality and quantity of the extracted DNA analyzed using Agarose gel electrophoresis and Picodrop respectively. Then, the 16S rdna gene of bacteria amplified through universal primer for preparing a genomic library by PCR. Results showed that the highest concentration and quality of extracted DNA was obtained by protocol D which was about 135 μg/ul and 260/230 = 2.2 respectively. Moreover, 500 bp fragment amplified perfectly by using DNA extracted through protocol D in the PCR test. Therefore, protocol D can be used as an appropriate and effective way in order to study the microbial population of oily soils using direct extraction of DNA.

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L

The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant^-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IF_H). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.

Effectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence

Issues concerning the use of harmful chemical fertilizers and pesticides that have large negative impacts on environmental and human health have generated increasing interest in the use of beneficial microorganisms for the development of sustainable agri-food systems. A successful microbial inoculant has to colonize the root system, establish a positive interaction and persist in the environment in competition with native microorganisms living in the soil through rhizocompetence traits. Currently, several approaches based on culture-dependent, microscopic and molecular methods have been developed to follow bioinoculants in the soil and plant surface over time. Although culture-dependent methods are commonly used to estimate the persistence of bioinoculants, it is difficult to differentiate inoculated organisms from native populations based on morphological characteristics. Therefore, these methods should be used complementary to culture-independent approaches. Microscopy-based techniques (bright-field, electron and fluorescence microscopy) allow to obtain a picture of microbial colonization outside and inside plant tissues also at high resolution, but it is not possible to always distinguish living cells from dead cells by direct observation as well as distinguish bioinoculants from indigenous microbial populations living in soils. In addition, the development of metagenomic techniques, including the use of DNA probes, PCR-based methods, next-generation sequencing, whole-genome sequencing and pangenome methods, provides a complementary approach useful to understand plant-soil-microbe interactions. However, to ensure good results in microbiological analysis, the first fundamental prerequisite is correct soil sampling and sample preparation for the different methodological approaches that will be assayed. Here, we provide an overview of the advantages and limitations of the currently used methods and new methodological approaches that could be developed to assess the presence, plant colonization and soil persistence of bioinoculants in the rhizosphere. We further discuss the possibility of integrating multidisciplinary approaches to examine the variations in microbial communities after inoculation and to track the inoculated microbial strains.

Microbiological and biochemical properties of soil polluted with a mixture of spiroxamine, tebuconazole, and triadimenol under the cultivation of Triticum aestivum L

Pesticide contamination is one of the most serious threats for agricultural soils. Excessive pesticide levels in soil can exert negative effects on soil-dwelling organisms by decreasing their bioavailability and, consequently, lowering soil quality. This study aimed to evaluate the effect of a mixture of spiroxamine, tebuconazole, and triadimenol (S + Te + Tr) on the biological activity of soil determined based on the proliferation of microorganisms and their diversity, enzymatic activity of soil, and resistance of Triticum aestivum L. A pot experiment was performed on sandy loam (pH 7.0) treated with four doses of the tested active ingredients: 0.000, 0.092, 2.76, 13.80, and 27.60 mg kg^-1. Soil without the fungicide served as the control sample. The tested fungicide induced changes in the biological activity of soil. When administered to the soil in the highest dose (27.60 mg kg^-1 DM of soil), it inhibited its biological activity. It significantly inhibited the proliferation of organotrophs, actinomycetes, and fungi, but still the most susceptible to its effects turned out to be fungi. Fungicide dose of 27.60 mg kg^-1 decreased counts of organotrophic bacteria, actinomycetes, and fungi by on average 0.009 log, 0.100 log, and 0.282 log, respectively, compared to the control sample. Administration of the S + Te + Tr mixture to soil decreased also values of colony development index (CD) determined for all tested groups of microorganisms. Values of the ecophysiological diversity index (EP) decreased in the case of organotrophs and actimomycetes and increased in the case of fungi. The S + Te + Tr mixture inhibited activities of dehydrogenases, urease, and acid phosphatase. Significant changes were also reported in the growth of spring wheat. The resistance index (RS) calculated based on plant yield demonstrated spring wheat to be very susceptible to the tested preparation administered to soil in doses of 13.80 and 27.60 mg kg^-1.

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition. To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers from 1.00 to 2.20 m. Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition. Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier. These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis

The sedimentary Marl mudstone soil is composed primarily of CaCO₃, and is an important pedologic and geomorphologic element known as Marl, extensively dispersed in slopes and ridges in the northern Negev Desert, Israel. The wide Marl soil-layer areas are barren, with well-developed streamsides and no perennial vegetation cover. Soil systems in the Negev Desert have been widely studied, yet very little information was collected on Marl soils, and even less on the microbiome present in the Negev. Thus, an evaluation of the microbial-community inhabitants in a Marl soil layer was conducted in an attempt to distinguish between Marl with surface green mat and bare Marl soil layer. Our objective was to investigate the microbiome and abiotic components of the upper layer (0-5 cm) of Marl and Marl-with-green-mat soil collected in the Negev Desert. Plate-counting enabled the estimation of fungal and bacterial population size, while nested polymerase chain reaction (nPCR) and Ion Torrent sequencing were used to analyze biological diversity. The results indicate significant differences in microbial biomass and microbial-community diversity between Marl and Marl-green mat, despite similar pH levels. Further study is needed to enhance understanding of the activity of the biotic components and their contribution to slope stabilization.

Factors affecting soil microbial biomass and functional diversity with the application of organic amendments in three contrasting cropland soils during a field experiment

The effects of soil type and organic material quality on the microbial biomass and functional diversity of cropland soils were studied in a transplant experiment in the same climate during a 1-year field experiment. Six organic materials (WS: wheat straw, CS: corn straw, WR: wheat root, CR: corn root, PM: pig manure, CM: cattle manure), and three contrasting soils (Ferralic Cambisol, Calcaric Cambisol and Luvic Phaeozem) were chosen. At two time points (at the end of the 1st and 12th months), soil microbial biomass carbon (C) and nitrogen (N) (MBC and MBN) and Biolog Ecoplate substrate use patterns were determined, and the average well color development and the microbial functional diversity indices (Shannon, Simpson and McIntosh indices) were calculated. Organic material quality explained 29.5–50.9% of the variance in MBC and MBN when compared with the minor role of soil type (1.4–9.3%) at the end of the 1st and 12th months, and C/N ratio and total N of organic material were the main parameters. Soil properties, e.g., organic C and clay content were the predominant influence on microbial functional diversity in particular at the end of the 12th month (61.8–82.8% of the variance explained). The treatments of WS and CS significantly improved the MBC and microbial functional diversity indices over the control in the three soils in both sampling periods (P < 0.05). These results suggest that the application of crop straw is a long-term effective measure to increase microbial biomass, and can further induce the changes of soil properties to regulate soil microbial community.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Optimisation of protocol for effective detachment and selective recovery of the representative bacteria for extraction of metagenomic DNA from Eucalyptus spp. woodchips

For some environments such as planktonic/aqueous environments, the separation of bacteria cells from eukaryotic cells prior to DNA extraction using filtration is relatively straightforward. However, for woodchips, the bacteria are attached/embedded within the wood matrix, which prevents easy removal of bacterial cells. In this study, a method for the selective extraction of DNA from bacteria inhabiting Eucalyptus spp. woodchips has been developed. The objective was to compare milled and unmilled woodchips processed via three detachment methods, viz., sonication, vortexing and shaking followed by filtration using Teflon filters according to three relevant criteria: DNA yield, DNA purity and quality of DNA. Highest DNA yield was obtained by milling and vortexing for 10 min (77.50 ± 5.17 ng/μl), followed by milling and vortexing for 2 min (61.00 ± 6.56 ng/μl), unmilled and vortexing for 10 min (38.67 ± 5.17 ng/μl) and milled and shaking for 2 h (31.62 ± 5.17 ng/μl). The lowest DNA yield was obtained by using unmilled woodchips and 5 min of sonication treatment (7.00 ± 1.22 ng/μl). There was no significant difference in DNA purity for milled or unmilled woodchips processed via the three detachment methods. Duration of cell detachment treatment did not significantly influence DNA yield and purity. Following optimisation experiments, it was possible to extract bacterial DNA using milled woodchips and 10 minute vortexing devoid of DNA from the host background and other associated eukaryotes and of sufficient quality and quantity for metagenomic analysis.

Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing

Background

Fertilization as one of the measures in restoring degraded soil qualities has been introduced on arid steppes in recent decades. However, the fertilization use efficiency on arid steppes varies greatly between steppe types and years, enhancing uncertainties and risks in introducing fertilizations on such natural system to restore degraded steppes.

Methods

The experiment was a completely randomized design with five fertilization treatments, 0 (Control), 60 kg P ha⁻¹ (P), 100 kg N ha⁻¹ (N), 100 kg N ha⁻¹ plus 60 kg P ha⁻¹ (NP), and 4,000 kg sheep manure ha⁻¹ (M, equaling 16.4 kg P ha⁻¹ and 81.2 kg N ha⁻¹). Soils were sampled from a degraded arid steppe which was consecutively applied with organic and inorganic fertilizers for three years. We analyzed the diversity and abundance of soil bacteria and fungi using high-throughput sequencing technique, measured the aboveground biomass, the soil chemical properties (organic carbon, available and total phosphorus, available and total nitrogen, and pH), and the microbial biomass nitrogen and microbial biomass carbon.

Results

In total 3,927 OTU (operational taxonomic units) for bacteria and 453 OTU for fungi were identified from the tested soils. The Ace and Chao of bacteria were all larger than 2,400, which were almost 10 times of those of fungi. Fertilizations had no significant influence on the richness and diversity of the bacteria and fungi. However, the abundance of individual bacterial or fungi phylum or species was sensitive to fertilizations. Fertilization, particularly the phosphorus fertilizer, influenced more on the abundance of the AMF species and colonization. Among the soil properties, soil pH was one of the most important soil properties influencing the abundance of soil bacteria and fungi.

Discussion

Positive relationships between the abundance of bacteria and fungi and the soil chemical properties suggested that soil bacteria and fungi communities in degraded steppes could be altered by improving the soil chemical properties through fertilizations. However, it is still not clear whether the alteration of the soil microbe community is detrimental or beneficial to the degraded arid steppes.

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil^® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin^® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.