Analysis Of Soil Microbial Communities Research Articles

From Residue to Resource: A Physicochemical and Microbiological Analysis of Soil Microbial Communities through Film Mulch-Enhanced Rice Straw Return Strategies

Promoting rice straw in situ return is an important strategy for improving soil quality. From 2018 to 2021, we investigated the effects of rice straw return with microbial agents and film covering technology on soil physical and chemical properties at different layer depths, as well as the soil microbial community structure, in Hunan, southern China. This study was designed to evaluate the effects of microbial agents (T1), film mulch covering (T2), and the application of microbial agents combined with film mulch (T3) on the soil physicochemical properties and microbial community after rice straw in situ return. The results show that, after three years of continuous treatment, T3 significantly increased the soil temperature by 17.76–22.97%, T2 significantly increased the water content by 34.27–46.23%, and T1 and T3 significantly increased the soil pH. The addition of microbial agents combined with film mulch resulted in a notable increase in both the number of OTUs and the Chao1 index of soil microorganisms. Additionally, the model of promoting rice straw in situ return (the application of a microbial agent combined with film mulch) was shown to promote the growth of beneficial soil microorganisms. RDA was used for the investigation, and the findings showed that soil microorganisms were significantly influenced by the TOC content, pH, and water content. These findings provide evidence of an effective method for accelerating the decomposition of late rice straw and guiding soil improvement in tobacco–rice rotation regions.

Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.

To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.

Construction of biochar-based organohalide-respiring bacterial agent for remediation of 2,4,6-trichlorophenol contaminated soil

Construction of an efficient bio-reductive dechlorination system remains challenging due to the narrow ecological niche and low-growth rate of organohalide-respiring bacteria during field remediation. In this study, a biochar-based organohalide-respiring bacterial agent was obtained, and its performance and effects on indigenous microbial composition, diversity, and inter-relationship in soil were investigated. A well-performing material, Triton X-100 modified biochar (BC600-TX100), was found to have the superior average pore size, specific surface area and hydrophicity, compared to other materials. Interestingly, Pseudomonas aeruginosa CP-1, which is capable of 2,4,6-TCP dechlorination, showed a 348 times higher colonization cell number on BC600-TX100 than that of BC600 after 7 d. Meanwhile, the dechlorination rate in soil showed the highest (0.732 d-1) in the BC600-TX100 bacterial agent than in the other agents. The long-term performance of the BC600-TX100 OHRB agent was also verified, with a stable dechlorination activity over six cycles. Soil microbial community analysis found the addition of the BC600-TX100 OHRB agent significantly increased the relative abundance of genus Pseudomonas from 1.53% to 11.2%, and Pseudomonas formed a close interaction relationship with indigenous microorganisms, creating a micro-ecological environment conducive to reductive dechlorination. This study provides a feasible bacterial agent for the in-situ bioremediation of soil contaminated organohalides. Environmental ImplicationHalogenated organic compounds are a type of toxic, refractory, and bio-accumulative persistent compounds widely existed in environment, widely detected in the air, water, and soil. In this study, we provide a feasible bacterial agent for the in-situ bioremediation of soil contaminated halogenated organic compounds. The application of biochar provides new insights for “Turning waste into treasure”, which meets with the concept of green chemistry.

Comparison and analysis of soil microbial communities in organic and conventional paddy fields by farming season

Interest in soil health and biodiversity conservation has become increasingly important. Consequently, studies comparing the chemical and biological characteristics of organic and traditional paddy soils have been increasing. Soil microorganisms are essential in nutrient cycling; however, their diversity is challenging to ascertain because of their environmental sensitivity and complex interactions. Particularly, in domestic rice cultivation, the soil undergoes multiple irrigation and drainage processes during crop growth, providing a diverse ecological environment for soil microorganisms. The objective of this study is to compare the microbial community and diversity between paddy soils in two agricultural systems. We selected organic and conventional paddy fields in Yangpyeong, Gyeonggi Province, and collected monthly samples from August to November 2022 for analysis. Bacteria and fungi were amplified from the 16S rRNA V3V4 region, ITS 3–4 region respectively, For the comparison of microbial diversity, Alpha diversity indices (Chao1, Shannon, Gini-Simpson indices) were analyzed. The results indicated genus-level differences in microbial communities, with the genera Mucor and Sirastachys exclusively present in organic paddy soils, while the genus Ustilaginoidea was exclusively found in conventional paddy soils. Among them, Ustilaginoidea is reported to be a fungus causing false smut disease, causing damage to crop growth and quality. Additionally, the comparison of microbial diversity between the two farming showed no significant differences (p>0.05). In conclusion, When the microbial communities present in both farming systems were examined, organic farming appeared to be more advantageous than conventional farming regarding crop disease and health. This study provides essential soil chemical and microbiological data for understanding the fundamental characteristics of paddy soils in South Korea.

Ti3C2Tx MXene nanosheets protect Torreya grandis against root rot disease

Root rot is a soil-borne disease primarily caused by fungi. The malady not only decrease the ability of absorbing water and nutrients, but also severely threat agricultural productivity. Recently, a new family member of two-dimensional (2D) transition metal carbide materials, MXene (Ti3C2Tx), has gained much interest as a promising approach to control fungi. However, the efficient use and mechanism of MXene in protecting plant against pathogenic fungus are still rarely reported. Here, the synthesized MXene were first characterized by the atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic light scattering (DLS), transmission electron microscopy (TEM) and X-ray photoelectron spectra (XPS). MXene application in soil obviously enhanced the root rot disease resistance of T. grandis. Soil microbial community analysis indicated that the abundance of Fusasium genus was decreased by 68.32% after MXene treatment. Further, MXene specially affected the permeability of Fusarium solani via damaging their cell membranes, thereby causing the disintegration and cell death of F. solani. In addition, MXene nanoflakes could transport into roots through T. grandis root air space, which resulted in the accumulation of lignin in roots via enhancing the expression and activities of lignin biosynthesis-related genes in T. grandis roots. Taken together, our finding pioneers comprehensive insights into the antifungal mechanism of MXene against F. solani and the efficiency use of MXene in protecting plant against pathogenic fungus, which will prompt the rapid development of nanotechnology in sustainable forestry.

Effect of long-term conservation tillage management on microbial diversity under Mediterranean rainfed conditions

Conservation Agriculture has been the subject of numerous studies for decades. However, its impact on the soil microbial community has often been overlooked. Recent studies have shed light on the changes in soil bacterial composition resulting from modifications in tillage practices, particularly when compared to conventional tillage methods. However, there is a lack of soil microbial community analysis conducted under conservation tillage and rainfed conditions in the Mediterranean basin. A metataxonomic approach was employed to assess the influence of 19 years (2004–2022) of minimum tillage (MT) and no-till (NT) practices, along with crop rotation, on the soil bacterial community at upper layers (15 cm depth). This field study involved three different seasonal moments throughout the year. Results revealed that both sampling time and tillage management significantly influenced the structure of the bacterial community, whereas no effect was observed due to the crop. May showed a higher taxonomic diversity than July and December, showing differences in some o fthe most abundant phyla, such as Actinobacteria, Firmicutes and Proteobacteria. On the other hand, the long-term application of NT was found to lead to a significant decrease in bacterial diversity, with lower abundances of the phyla Chloroflexi, Gemmatimonadetes, and Armatimonadota, as well as an increase in k-strategist bacteria compared to MT. However, no significant effect on alpha diversity was observed as a result of tillage. no variations in phyla composition were observed attributable to crop, as the primary distinctions were identified among legume crops, which were associated with different sampling times. Therefore, our conclusion is that over this period, NT did not promote microbial diversity in the upper soil layers, despite notable shifts in bacterial composition occurring across seasonal time points in both tillage management systems.

EDNA metabarcoding analysis reveals the consequence of creating ecosystem‐scale refugia from deer grazing for the soil microbial communities

AbstractUngulate overbrowsing is a growing problem in forests worldwide due to its prolonged and pervasive impact on plant biodiversity and ecosystem functioning. It has been shown that overbrowsing not only reduces plant species diversity and biomass (i.e., direct effects) but also causes a loss of associated trophic levels that could potentially feedback to influence plant community structure (i.e., indirect effects). One of the primary pathways of such indirect effects that have not been fully examined is the impact of overbrowsing on soil microorganisms. Recent studies have shown that soil microorganisms maintain vegetation diversity and drive succession, so it is of critical importance to understand how soil microbial communities might be affected by or protected from the deer impact. To assess the consequence of creating artificial grazing refugia on the structure and composition of soil microbial communities, we compared the distribution and abundance of soil microbial taxa (bacteria, archaea, fungi) at the fenced versus unfenced control sites in the context of a catchment‐scale field experiment in Japan. The eDNA metabarcoding analysis of soil microbial communities showed that the numbers of archaea and basidiomycetes fungal species were greater in the fenced site than in the control, while no such pattern was found for bacteria and ascomycetes fungi. Despite the lack of significant influence of the fence treatment on taxonomic composition in the soil fungal communities, their functional guild composition was influenced by the fenced treatment, with significant changes in the abundance of animal pathogens. Thus, although the effect of fencing on soil microbial communities is characterized by complex responses that vary from taxon to taxon, our work suggests that creating ecosystem‐scale refugia from deer overgrazing might help sustain certain, if not all, taxa of soil microbial communities.

DNA sequencing, microbial indicators, and the discovery of buried kimberlites

Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Reduced graphene oxide accelerates the dissipation of 14C-Triclosan in paddy soil via adsorption interactions

Reduced graphene oxide (RGO) is one of common carbon nanomaterials, which is widely used in various fields. Triclosan is an antimicrobial agent added in pharmaceuticals and personal care products. Extensive release of RGO and triclosan has posed potential risks to humans and the environment. The impact of RGO on the fate of triclosan in paddy soil is poorly known. 14C-Triclosan was employed in the present study to determine its distribution, degradation and mineralization in paddy soil mixed with RGO. Compared with the control, RGO (500 mg kg−1) significantly inhibited the mineralization of 14C-triclosan, and reduced its extractability by 6.5%. The bound residues of triclosan in RGO-contaminated soil (100 and 500 mg kg−1) were 2.9–13.3% greater than that of the control at 112 d. RGO also accelerated the dissipation of triclosan, and its degradation products in both treatments and controls were tentatively identified via 14C-labeling method and LC-Q-TOF-MS analysis. The concentrations of the major metabolites (methyl-triclosan and dechlorinated dimer) were inversely related with the concentrations of RGO. RGO at 50 mg kg−1 or lower had a negligible effect on the degradation of triclosan in paddy soil. Triclosan was strongly adsorbed onto RGO-contaminated soil, which may play a vital role in the fate of triclosan in RGO-contaminated paddy soil. Interestingly, RGO had little effect on triclosan-degrading bacteria via soil microbial community analysis. This study helps understand the effects of RGO on the transformation of triclosan in paddy soil, which is of significance to evaluate the environmental risk of triclosan in RGO-contaminated soil.

A novel P nanofertilizer has no impacts on soil microbial communities and soil microbial activity

The aim of this work was to assess the impact of a novel P nanofertilizer (P-NF) on P solubility, microbial toxicity, soil respiration rate, soil enzyme activity and soil microbial community composition of two soils with contrasting properties in a laboratory incubation study. From the comparison with a commercial triple superphosphate (TSP), the P-NF induced lower release of soluble P, did not cause microbial toxicity, nor reduced soil respiration. Among the measured enzyme activities involved in C, N, P and S mineralization, only the protease activity was significantly inhibited by the P-NF in both the studied soils. Analysis of soil microbial communities showed no significant impacts on bacteria, fungi and archaea, after 1 and 7 d of incubation. We concluded that the tested novel P-NF could be safely used in agriculture.

Composition and characteristics of soil microbial communities in cotton fields with different incidences of Verticillium wilt

ABSTRACT Soil microorganisms could affect the growth of plants and play an important role in indicating the change of soil environment. Cotton Verticillium wilt is a serious soil borne disease. This study aimed to analyze the community characteristics of soil microorganisms in cotton fields with different incidences of Verticillium wilt, so as to provide theoretical guidance for the prevention and control of soil borne diseases of cotton. Through the analysis of soil microbial communities in six fields, the results showed that there was no difference in fungal and bacterial alpha-diversity index before cotton planting, while there were differences in rhizosphere of diseased plants. For fungal beta diversity indexes, there were significant differences in these six fields. There was no significant difference for bacterial beta diversity indexes before cotton planting, while there was a certain difference in the rhizosphere of diseased cotton plants. The composition of fungi and bacteria in different fields was roughly the same at the genus level, but the abundances of the same genus varied greatly between different fields. Before cotton planting, there were 61 fungi (genera) and 126 bacteria (genera) with different abundances in the six fields. Pseudomonas, Sphingomonas and Burkholderia had higher abundances in the fields with less incidence. This study will provide a theoretical basis for microbial control of Cotton Verticillium wilt.

Clustering analysis of soil microbial community at global scale

In the soil there are huge numbers of bacteria, and their function affect soil properties, also they are a part of the microbiome. How soil microbiomes are different throughout the world and how they relate to the region and the environment is of major interest. Recently, the development of next-generation sequencing has enabled researchers to accumulate metagenomic profile data, and perform large-scale and comprehensive microbiome analyses. In this study, we analysed the data from various environments worldwide using the microbiome database, the earth microbiome project (EMP). Based on UniFrac distance we performed the clustering analysis. The results interpreted according to the bacterial functions and characteristics. The group of bacteria related to paddy, vineyard, grasslands in Mongolian, forests, and biofilter. Furthermore, we investigated the relationship between clusters and climate zones. This research is expected to lead to knowledge of soil management based on the soil microbiome.

Clustering analysis of soil microbial community at global scale

Clustering analysis of soil microbial community at global scale

Cell-Free Fermentation Broth of Bacillus velezensis Strain S3-1 Improves Pak Choi Nutritional Quality and Changes the Bacterial Community Structure of the Rhizosphere Soil.

Bacillus velezensis is a plant growth-promoting rhizobacteria (PGPR) that has long been proven to improve the growth of plants, and it has been widely used in agriculture. However, in many reports, we observed that during the application of bacterial fluids, it appeared that the effect of the cell-free fermentation broth (CFB) was ignored. The purpose of this study is to compare the effect of the no inoculation treatment (CK), the B. velezensis strain S3-1 treatment (S), the CFB treatment in the Pak choi, soil bacterial community structure, soil enzyme activity, and field soil properties. The results have shown that, compared to the inoculation B. velezensis strain S3-1 treatment and the no-inoculation treatment; the inoculation of the CFB treatment can significantly enhance the soluble protein, soluble solids, ascorbic acid of Pak choi and increase the total phosphorus content and electrical conductivity (EC) in the soil. Based on high-throughput sequencing data, our analysis of soil microbial communities used R, NETWORK, and PICRUSt showed that the CFB treatment can enhance the relative abundance of Acidobacteria in the soil, decrease the abundance of native Bacillus in the soil, change the microbial community structure of the top 50 operational taxonomic units (OTUs), and improve soil microbial carbon metabolism and nitrogen metabolism. Overall, we observed that CFB treatment can also improve plant nutrition and change soil microbial communities. This study provides new insights for the application of microbial fertilizers in agricultural production.

Metagenomic analysis of soil microbial community under PFOA and PFOS stress

Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.

Taxonomic and functional analysis of soil microbial communities in a mining site across a metal(loid) contamination gradient

AbstractSoil microorganisms surviving in mining sites have developed metal‐resistance mechanisms to biotransform metals. Their use as biofertilizers can improve phytoremediation efficiency in contaminated soils by reducing metal toxicity while promoting plant growth. We analysed through whole‐metagenome shotgun sequencing the composition, diversity and function of microbial communities present in a contaminated mine soil along a gradient of metals (As, Cu, Fe, Mn, Pb, Zn) to identify tolerant species carrying metal‐resistance functional genes that can be used in association with plants for phytoremediation. Soil samples were collected from an abandoned copper mine, across three areas with different levels of metal contamination (unaffected, moderately contaminated and highly contaminated). The relative abundance of Proteobacteria, especially genus Bradyrhizobium, increased in the highly contaminated area, whereas Actinobacteria dominated in the unaffected area. Archaea (Euryarchaeota) predominated in the moderately contaminated area, Haloarcula, Halobacterium and Halorubrum being the most abundant genera. The fungi Basidiomycota did not exhibit differences among the areas, whereas Ascomycota, especially the genus Aspergillus, increased in areas with low metal concentrations. Metal‐resistance genes associated with Fe (acn, furA, dpsA), Cu (cop‐unnamed, copF, actP, copA, mmco, cutO) and As (arsT, arsC, aioA/aoxB) metabolism were the most abundant and were affected by the gradient of soil contamination. Those associated with Cu predominated in the most contaminated area, whereas As and Fe genes were more abundant in the least contaminated. Among the carriers of these metal‐resistance genes, Bradyrhizobium diazoefficiens, Pseudomonas aeruginosa, Halorubrum trapanicum, Aspergillus fumigatus and A. fischeri were dominant in the most contaminated area. These species could give rise to promising biofertilizers to be used in association with suitable plants for the phytoremediation of contaminated mining sites.Highlights Metals affect differentially abundance, diversity and function of microorganisms in a mine soil. Proteobacteria dominated in contaminated areas and Actinobacteria in the less contaminated. Most abundant metal‐resistance genes were associated with Cu, As and Fe. Bradyrhizobium diazoefficiens and other species are promising biofertilizers for phytoremediation.

Metagenomics analysis of soil microbial communities in plant agroforestry system rubber tree (Hevea brasiliensis) – Ganyong (Canna sp.)

Rubber tree (Hevea brasiliensis) is one of important industrial plants in Indonesia. It is planted widely in some provinces in Indonesia, one of which is in West Java under management of the PTPN VIII plantation, Subang Regency. Intercropping system using underutilized crops Canna sp. (Ganyong) had been introduced on Rubber plantation. The aim of this research is to analyze the diversity, abundance and richness of rhizosphere soil microbial under rubber-canna agroforestry system using metagenomic analysis of 16S rRNA gene of soil rhizosphere bacteria. The research was carried out by collecting soil samples from 2 different soil conditions (soils with Canna (G) and soils without Canna (TG)). 2 different soil depths conditions (20 and 40 cm) were also investigated. The results showed that number of microbial in G soils was found more abundance than in TG soils, while based on soil depth there was no significant effect on soil microbial abundance. Based on class level was found 84 Classes. There were 3 classes that are mostly found in G and TG, namely Ktedonobacteria, Acidobacteria and Planctomycetia. Microbial diversity in family level mostly found in G and TG, Namely Koribacteraceae, Gemmataceae, Synobacteraceae, Hyphomicrobiaceae.

Composted biosolids for golf course turfgrass management: Impacts on the soil microbiome and nutrient cycling

Land application of biosolids is a primary means of recycling human waste products globally; however, because biosolids are also heavily enriched with nutrients and pollutants, it is necessary to consider the environmental impacts of land applications in various agro-ecosystems. To reduce costs and divert waste, biosolids from Joint Base Lewis-McChord, a military installation south of Tacoma, WA, USA, are composted with organic materials derived from the base itself. The potential for turfgrass management using the composted biosolids was tested in a field study at the military recreation facility, Eagles Pride golf course. The composted biosolids were surface-amended to golf course fairways (n = 3) at a rate of 46 Mg ha−1, in split applications, fall and spring, over two years, 2015 and 2016. Soil bacterial and fungal community responses were evaluated in amended and unamended soils from each fairway, along with soil chemical properties, including soil pH, total carbon (C), total nitrogen (N), and the C:N ratio. Soil microbial community analysis on soils sampled pre- and post-amendment did not demonstrate changes in community structure as a result of the composted biosolids application. Differences observed in soil microbial community structure appears to reflect edaphic and vegetative differences between fairways. Generally, correlations between soil properties and bacterial community OTUs were stronger than those with fungal OTUs, and predicted bacterial community functional analysis revealed several KO term groups were significantly correlated with soil TC and TN. Turfgrass biomass was unaffected, while leaf tissue N was increased by 4.5 and 10.6% in 2015 and 2016, respectively. These results suggest that amendment with composted biosolids does not strongly impact microbial communities across two years; however, long-term amendment could have affects that are not detected during this short-term study.

Analysis of soil microbial communities based on amplicon sequencing of marker genes

The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.