Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields

Local microbial yield-associating signatures largely extend to global differences in plant growth

Rapid advancements in high-throughput DNA sequencing have opened new avenues for applying microbiome-based machine learning to predict and model determinants that enhance agricultural productivity and sustainability in agroecosystems. Although early attempts have been made to predict crop yield or measures of soil health through the soil microbiome, it is unclear if microbial patterns associated with plant growth or crop yield on a local scale can be generalized to predict differences in plant growth on a continental or global scale. Herein, we measured the soil bacterial microbiome on a single maize field in Germany with high spatial sampling resolution and correlated the community composition with corresponding volume flow-based high-resolution yield measurements. Applying machine learning techniques, a least absolute shrinkage and selection operator (LASSO) regression model could retrospectively predict ∼65 % of variation in maize yield through cross-validation. We validated this locally trained model, comprising 26 genera, using data from seven publicly available datasets. Predictions from this model correlated with various yield or plant growth metrics throughout the world and could predict up to 37 % of variation in global vegetation, as assessed by normalized difference vegetation index data. Further feature inspection showed that the genera Hyphomicrobium, Luedemannella, Reyranella, JGI.0001001.H03, Aeromicrobium, Flavitalea and Ellin6055 most consistently contributed to plant growth prediction. Finally, repeating LASSO regression, an optimized model could predict up to 50 % of variation in global vegetation. In summary, our data suggests a globally conserved set of soil bacterial taxa that correlates with vegetation and might be used to predict plant growth.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Organic Farming Enhances Diversity and Recruits Beneficial Soil Fungal Groups in Traditional Banana Plantations

This study investigates the impact of organic (OF) and conventional farming (CF) on soil fungal communities in banana monoculture plantations on Madeira Island. We hypothesized that OF promotes beneficial fungal groups over harmful ones, sustaining soil health. Soil samples were collected from six plantations (three OF and three CF) for ITS amplicon sequencing to assess fungal diversity. Results showed that OF significantly enhanced fungal alpha-diversity (Shannon-Wiener index) and Evenness. The phylum Ascomycota dominated OF systems, while Basidiomycota prevailed in CF. Mortierella, a beneficial genus, was abundant in OF and is observed in CF but was less evident, being the genus Trechispora the most well represented in CF agrosystems. Additionally, OF was associated with higher soil pH and Mg levels, which correlated positively with beneficial fungal groups. Functional analysis revealed that OF promoted saprotrophic fungi, crucial for the decomposition of organic matter and nutrient cycling. However, both systems exhibited low levels of arbuscular mycorrhizal fungi, likely due to high phosphorus levels. These findings suggest that organic practices can enhance soil fungal diversity and health, although attention to nutrient management is critical to further improving soil-plant-fungi interactions.

Association of Atrazine-Induced Overexpression of Aldo-Keto-Reductase 1C2 (AKR1C2) with Hypoandrogenism and Infertility: An Experimental Study in Male Wistar Rat

Atrazine (ATZ, C8H14ClN5) is a widely used synthetic herbicide that contaminates drinking water. It is a known endocrine disruptor that disrupts various molecular pathways involved in hormone signaling, and DNA damage, and can cause reproductive disorders, including decreased fertility, and abnormal development of reproductive organs, as revealed in animal model studies. However, the effect of ATZ on steroidogenesis in the male reproductive system, especially reduction of ketosteroids to hydroxysteroids, remains unclear. This study investigated the toxicity of ATZ on the male reproductive system in the Wistar rat model, with an emphasis on its adverse effect on aldo-ketoreductase family 1 member C2 (AKR1C2). Male Wistar rats were administered ATZ for 56 days (duration of one spermatogenic cycle) through oral route, at 20, 40 and 60 mg/kg body weight (bw) doses. The results indicate that ATZ exposure affects the body weight, impairs sperm production, and decrease FSH, LH, and testosterone levels. Additionally, the down-regulation of key steroidogenic enzymes by ATZ disrupted the synthesis of testosterone, leading to decreased levels of this essential male hormone. On the other hand, the expression of AKR1C2 (mRNA and protein) in the testis was upregulated. The findings suggest that AKR1C2 plays a role in androgen metabolism. Furthermore, its overexpression may lead to alteration in the expression of genes in the connected pathway, causing an increase in the breakdown or inactivation of androgens, which would result in lower androgen levels and, thereby, lead to hypoandrogenism, as the combined effects of down-regulation of steroidogenic genes and up-regulation of AKR1C2. These findings reveal direct implication of disrupted AKR1C2 in male reproductive health and highlight the need for further research on the impact of environmental toxins on human fertility, ultimately providing for better patient care.

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.

Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks

Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.

Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem

The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.

Soil quality and microbial communities in subtropical slope lands under different agricultural management practices

Land degradation is a major threat to ecosystem. Long-term conventional farming practices can lead to severe soil degradation and a decline in crop productivity, which are challenging for both local and global communities. This study was conducted to clarify the responses on soil physicochemical properties and microbial communities to changes in farming practices. Slope land orchards under three agricultural management practices-conventional farming (CF), organic farming (OF), and ecofriendly farming (EFF)-were included in this study. We found that soil carbon stock increased by 3.6 and 5.1 times in surface soils (0-30 cm) under EFF and OF treatments, respectively. EFF and OF significantly increased the contents of total nitrogen by 0.33-0.46 g/kg, ammonia-N by 3.0-7.3 g/kg, and microbial biomass carbon by 0.56-1.04 g/kg but reduced those of pH by 0.6 units at least, and available phosphorous by 104-114 mg/kg. The application of phosphorous-containing herbicides and chemical fertilizers might increase the contents of phosphorous and nitrate in CF soil. High abundances of Acidobacteria and Actinobacteria were observed in EFF and OF soils, likely because of phosphorous deficiency in these soils. The abundance of fungi in OF soil indicated that plants' demand for available soil phosphorous induced the fungus-mediated mineralization of organic phosphorous. High abundances of Gammaproteobacteria, Planctomycetes, Firmicutes, and Nitrospirae were observed in CF soil, possibly because of the regular use of herbicides containing phosphorous and chemical fertilizers containing high total nitrogen contents.

Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil

Introduction

Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems.

Methods

The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu'er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology.

Results

Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations' keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH4 + negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index.

Conclusion

In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network.

Agricultural soil physico-chemical parameters and microbial abundance and diversity under long-run farming practices: A greenhouse study

The growth of agriculture led to indiscriminate use of synthetic pesticides or fertilizers and unsustainable crop management farming practices which can aggravate harmful impacts on the microbial population and physical and chemical characteristics of soil ecosystem. Based on this fact, the present study was planned to evaluate the effect of long run farming practices on different soil physico-chemical parameters and soil microbial abundance and diversity within different soil depth (0–20 cm and 20–40 cm) at Quzhou Experimental Station of China Agricultural University, Hebei, China during October and December, 2016. The effect of farming practices on soil microbial abundance and diversity was studied by phospho-lipid fatty acid (PLFA) and DNA high-throughput sequencing methods. The findings revealed that soil is neutral to slightly alkaline in nature with highest water content under organic farming (ORF) at 0–20 cm and least under conventional farming at 20–40 cm depth. It was found that the ORF significantly increased the contents of total organic carbon (TOC), total carbon (TC), ammonium nitrogen, available nitrogen (AN), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) followed by low input and conventional farming modes in both October and December soil samples. The correlation analysis showed significantly (at p ≤ 0.05 and 0.01) strong positive relationship within different physical and chemical properties of the soil under study. ANOVA and MANOVA analysis indicated significant effect of interaction between soil depth and farming modes on soil parameters. PCA analysis showed the most significant correlation between most of the bacterial types (G + bacteria, G− bacteria, actinomycetes) and soil AP, total available nitrogen, TOC and soil WC. Pearson correlation analysis revealed a significant correlation between microbial phylum groups (Proteobacteria, Bacteroidetes, and Latescibacteria) and microbial class group (Alphaproteobacteria, Sphingobacteriia, Flavobacteriia) with most of the soil physicochemical properties.

High-throughput sequencing reveals rhizosphere fungal community composition and diversity at different growth stages of Populus euphratica in the lower reaches of the Tarim River

Background

Populus euphratica is one of the most ancient and primitive tree species of Populus spp and plays an important role in maintaining the ecological balance in desert areas. To decipher the diversity, community structure, and relationship between rhizosphere fungi and environmental factors at different growth stages of P. euphratica demands an in-depth investigation.

Methods

In this study, P. euphratica at different growth stages (young, medium, overripe, and decline periods) was selected as the research object, based on the determination of the physicochemical properties of its rhizosphere soil, the fungal community structure and diversity of P. euphratica and their correlation with soil physicochemical properties were comprehensively analyzed through high-throughput sequencing technology (internal transcribed spacer (ITS)) and bioinformatics analysis methods.

Results

According to the analysis of OTU annotation results, the rhizosphere soil fungal communities identified in Populus euphratica were categorized into10 phyla, 36 classes, 77 orders, 165 families, 275 genera and 353 species. The alpha diversity analysis showed that there was no obvious change between the different growth stages, while beta diversity analysis showed that there were significantly differences in the composition of rhizosphere soil fungal communities between mature and overripe trees (R ² = 0.31, P = 0.001), mature and deadwood (R ² = 0.28, P = 0.001). Ascomycota and Basidiomycota were dominant phyla in the rhizosphere fungal community and the dominant genera were Geopora, Chondrostereum and unidentified_Sordariales_sp. The relative abundance of the top ten fungi at each classification level differed greatly in different stages. Canonical correspondence analysis (CCA) and Spearman's correlation analysis showed that conductivity (EC) was the main soil factor affecting the composition of Populus euphratica rhizosphere soil fungal community (P < 0.01), followed by total dissolvable salts (TDS) and available potassium (AK) (P < 0.05).

Conclusions

Our data revealed that the rhizosphere fungal communities at the different growth stages of P. euphratica have differences, conductivity (EC) was the key factor driving rhizosphere fungi diversity and community structure, followed by total dissolvable salts (TDS) and available potassium (AK).