The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices

Microbiome Migration from Soil to Leaves in Maize and Rice

The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant-microbe interactions for sustainable agriculture.

Monitoring of indicators and bacterial succession in organic-amended technosols for the restoration of semiarid ecosystems

Restoration of mining sites is essential to ensure ecosystem services and biodiversity. One restoration strategy employed in arid and semi-arid zones is the use of organic amendments to establishment technosols. However, it is necessary to monitor the restoration progress in order to select appropriate amendments. This study monitored the effects of compost gardening, greenhouse horticulture and stabilized sewage sludge, and their blends. We focused on soil physical and chemical indicators and bacterial community structure and diversity during the 30 months after application. Organic amendments increased total organic carbon and nitrogen within six months, staying elevated compared to natural soils over 30 months. Electrical conductivity rose then stabilized, the pH slightly decreased but stayed alkaline, and water holding capacity improved in treated technosols. Bacterial diversity increased in amended technosols compared to control. Alpha diversity varied with treatment and time, peaking at 18 months. Technosols with plant compost showed reduced bacterial richness at 30 months, while those with sewage sludge and its mixtures maintained it. The bacterial community analysis showed significant differences among treatments and times, highlighting dominant phyla like Proteobacteria and Bacteroidetes. PCoA analysis showed clear separation of bacterial communities from treated, natural, and control soils, with notable differences between plant and sludge treatments. Soil variables such as TOC, TN, EC and water holding capacity explained more than 82 % of the variation in bacterial communities. Eighty-three indicator taxa were identified that explained the differences between the microbial communities of treated and untreated soils, highlighting the importance of taxa such as Pelagibacterium spp., Roseivirga spp. and Cellvibrio spp. in preserving soil health. In short, organic amendments improve soil properties and promote the diversity and stability of beneficial microbial communities in semi-arid mined soils, underlining their crucial role in the restoration and long-term maintenance of degraded soils.

Ecological practices increase soil fertility and microbial diversity under intensive farming

Intensive farming offers a potential solution to feed the growing population due to its high productivity. Conventional management (CO) based on inorganic fertilization practices degrades soil quality, but restorative practices including ecological intensification (EI) and organic management results in maintaining soil quality without compromising productivity. In this paper, two different management systems were evaluated: CO, based on inorganic fertilization, and EI, focused on providing organic nutrients to soils to support crops. EI increased soil fertility, together with higher alpha diversity indices, more differentially abundant amplicon sequence variant (ASVs) (247 EI vs. 165 CO) and indicator taxa (60 EI vs. 32 CO). Distinct bacterial taxa were associated with the different management systems, revealing their roles in soil processes and nutrient availability. In the CO treatment, indicator genera such as Nitrospira and Desulfarculaceae were linked to N fertilization and nitrite oxidation, while RB41 was associated with phosphorus availability. Ammoniphilus, PAUC26f, and BSV26 were also indicators of CO management. Conversely, EI treatment promoted bacteria involved in organic matter decomposition and nutrient cycling, such as Halomonas, Chryseolinea and Rhodobacteraceae. Gemmatimonas, Steroidobacter, Altererythrobacter, Acidibacter and Anseongella contribute to carbon and nitrogen cycling. Burkholderiaceae and Rhodopirellula play roles in phosphate solubilization and organic P mineralization, respectively. Numerous taxa with plant growth-promoting (PGP) attributes, such as BIrii41, Pseudomonas, and Lysobacter, were also identified as indicators of the EI treatment. EI associated bacteria were positively correlated with soil organic carbon contents, nitrates, and exchangeable bases, while negatively correlated with CO bacteria. A distance-based multivariate multiple regression (DistLM) demonstrated a strong relationship (r2 = 0.78) between soil physicochemical variables and bacterial community structure, with SOC explaining the most variations in the model. Other significant parameters included potassium (K), electrical conductivity (EC), and nitrates. The results suggest that EI promotes more sustainable soils in terms of fertility and microbial diversity.

Glucose addition in natural forest soils has higher biological nitrogen fixation capacity than other types of soils

Land use changes soil microbial and chemical properties, but the mechanism of biological nitrogen fixation under different land use patterns is rarely reported, so we used four types of soil: Natural forest soil (NS), healthy banana soil (HS), diseased banana soil (DS) and paddy soil (PS). Treatments included the control (CK), addition of glucose (G), addition of glucose and ammonium nitrate (GN), addition of banana straw (BS), addition of banana straw and ammonium nitrate (BSN), addition of banana root (BR), and addition of banana root and ammonium nitrate (BRN). The study found that the change of soil utilization types, glucose addition increased carbon dioxide emissions (Compared with the control, increased by 963.11%, 508.39%, 794.77% and 511.34%, respectively) and enhanced the ability of soil microbial nitrogen fixation. Importantly, natural forest soil microorganisms have a higher biological nitrogen fixation capacity compared to other types of soils. Glucose addition caused the accumulation of ammonium nitrogen (Compared with the control, increased by 426.08%, 934.21%, 420% and 1065.95%, respectively), indicating that microorganisms had higher utilization efficiency of soluble carbon and enhanced the biological nitrogen fixation capacity, and nitrogen addition caused the accumulation of ammonium nitrogen, thereby weakening the biological nitrogen fixation capacity. At the same time, glucose significantly increased the Fimicutes phylum (83.73%, 66.38%, 67.18% and 70.36%) and lowered the level of other bacterial phylums, thereby reducing the bacterial network structure, and the stability of the soil environment has decreased. Forest analysis showed that CO2 was an important factor in predicting the bacterial community structure of different soil types, an increase in CO2 content can predict drastic changes in the bacterial community. Bacteria at the Fimicutes phylum level preferred glucose, which may also have a negative effect on bacteria at the level of other phylums.

Understanding the interactions of genotype with environment and management (G×E×M) to enhance maize productivity in Conservation Agriculture systems of Malawi

Climatic variability and soil fertility decline present a fundamental challenge for smallholder farmers to determine the optimum management practices in the production of maize. Optimizing genotype (G) and management (M) of maize under different environmental conditions (E) and their interactions are essential for enhancing maize productivity in the smallholder sector of Malawi where maize is the main staple food. Here, we evaluated over seven seasons, the performance of four commercial maize genotypes [including hybrids and one open pollinated variety (OPV)] managed under different Conservation Agriculture (CA) and conventional practices (CP) across on-farm communities of central and southern Malawi. Our results revealed significant G×E and E×M interactions and showed that hybrids such as DKC 80-53 and PAN 53 outyielded the other hybrid and the OPV in most of the environments while the OPV ZM523 had greater yields in environments with above-average rainfall and shorter in-season dry spells. These environments received a maximum of 1250 mm to 1500 mm of rainfall and yet the long-term averages were 855 mm and 1248 mm, respectively. Despite yielding lower, the OPV ZM523 also exhibited higher yield stability across environments compared to the hybrid MH 30, possibly due to its resilience to drought, heat stress, and low soil fertility conditions which are often prevalent in the target communities. Conservation Agriculture-based practices outyielded CP across the genotypes and environments. However, amongst the CA-based systems, intercropping of maize with pigeonpea [Cajanus cajan (L.) Millsp] and cowpea (Vigna unguiculata Walp.) performed less than monocropping maize and then rotating it with a legume probably due to competition for moisture between the main and the companion crops in the intercrop. The key findings of this study suggest the need to optimize varietal and management options for particular environments to maximize maize productivity in Malawi. This means that smallholder farmers in Malawi should adopt hybrids and CA-based systems for enhanced yields but could also consider OPVs where the climate is highly variable. Further rigorous analysis that includes more abiotic stress factors is recommended for a better understanding of yield response.

Conservation tillage practices affect soil microbial diversity and composition in experimental fields

Introduction

Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments.

Methodology

Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments.

Results and discussion

Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased.

Conclusion

The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.

Land-use change alters the bacterial community structure, but not forest management

Deforestation has a large impact on soil fertility, especially on steep slopes, but by applying sustainable management practices, local communities in Oaxaca (Mexico) have tried to avoid the most negative effects on the forest ecosystems they manage. In this study, the characteristics and bacterial community structure were investigated from soil sampled in triplicate (n = 3) with different land use, i.e., arable, natural forest, sustainable managed, and reforested soil. The pH was significantly higher in the arable (6.2) than in the forest soils (≤ 5.3), while the organic matter was > 2 times higher in the natural forest (80.4 g/kg) and sustainable managed soil (86.3 g/kg) than in the arable (36.8 g/kg) and cleared and reforested soil (39.3 g/kg). The higher organic matter content in the first two soils was due to leaf litter, absent in the other soils. The species richness (q = 0), the typical (q = 1) and dominant bacteria (q = 2) were not affected significantly by land use. The beta diversity, however, showed a significant effect of land use on species richness (p = 0.0029). Proteobacteria (40.135%) and Actinobacteria (20.15%) were the dominant bacterial phyla, and Halomonas (14.50%) and the Verrucomicrobia DA101 (3.39%) were the dominant genera. The bacterial communities were highly significantly different in soil with different land use considering the taxonomic level of genus and OTUs (p ≤ 0.003). It was found that the sustainable managed forest provided the local community with sellable wood while maintaining the soil organic matter content, i.e., sequestered C and without altering the bacterial community structure.

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

Background

Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study.

Results

In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice.

Conclusions

Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02648-1.

Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems

Despite the central role of microorganisms in soil fertility, little understanding exists regarding the impact of management practices and soil microbial diversity on soil processes. Strong correlations among soil microbial composition, management practices, and microbially mediated processes have been previously shown. However, limited integration of the different parameters has hindered our understanding of agroecosystem functioning. Multivariate analyses of these systems allow simultaneous evaluation of the parameters and can lead to hypotheses on the microbial groups involved in specific nutrient transformations. In the present study, using a multivariate approach, we investigated the effect of microbial composition (16SrDNA sequencing) and soil properties in carbon mineralization (C_MIN) (BIOLOG™, Hayward, CA, USA) across different management categories on coffee agroecosystems in Mexico. Results showed that (i) changes in soil physicochemical variables were related to management, not to region, (ii) microbial composition was associated with changes in management intensity, (iii) specific bacterial groups were associated with different management categories, and (iv) there was a broader utilization range of carbon sources in non-managed plots. The identification of specific bacterial groups, management practices, and soil parameters, and their correlation with the utilization range of carbon sources, presents the possibility to experimentally test hypotheses on the interplay of all these components and further our understanding of agroecosystem functioning and sustainable management.

Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study

To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.

Tillage Practices and Residue Management Manipulate Soil Bacterial and Fungal Communities and Networks in Maize Agroecosystems

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly impacted in 2018. Soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on soil microbial co-occurrence networks, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community and simplified soil bacterial and fungal networks in 2018. This study highlights the dissimilar responses of bacterial and fungal networks to tillage practices and emphasizes that tillage practice is more important than residue management in shaping soil microbial communities.

Responses of CO2 emissions and soil microbial community structures to organic amendment in two contrasting soils in Zambia

In sub-Saharan Africa, efforts have been made to increase soil carbon (C) content in agricultural ecosystems due to severe soil degradation. The use of organic materials is a feasible method for recovering soil organic C; however, the effects of organic amendments on soil microbial communities and C cycles under C-limited soil conditions are still unknown. In this study, we conducted field experiments in Zambia using organic amendments at two sites with contrasting C content. At both sites, temporal changes in soil carbon dioxide (CO₂) emissions and prokaryotic community structures were monitored during the crop growing season (126 days). The organic amendments increased CO₂ emissions and prokaryotic abundance at the Kabwe site, whereas no direct impacts were observed at the Lusaka site. We also observed a larger temporal variability in the soil microbial community structure at Kabwe than that at Lusaka. These contrasting results between the two soils may be due to the microbial community stability differences between each site. However, as organic amendments have considerable potential to enhance microbial abundance and consequently sequester C at the Kabwe site, site-specific strategies are required to address the issues of soil C depletion in drylands.

Effects of Residue Retention and Removal Following Thinning on Soil Bacterial Community Composition and Diversity in a Larix olgensis Plantation, Northeast China

Thinning is an important management practice for reducing plant competition and improving wood production in forests. The residues from thinning can contain large amounts of carbon (C) and nitrogen (N), and the management methods applied directly after thinning can affect the input of nutrients to soil, change the availability of substrates to soil bacterial communities, and thus affect soil bacterial community structure. Our objective was to determine the effects of different thinning residue treatments on soil bacterial community structure and diversity. Illumina high-throughput sequencing technology was used to sequence the bacterial 16SrRNA V3–V4 variable region of the soil (0–10 cm) of a Larix olgensis plantation to compare the composition and diversity of soil bacterial communities following removal of thinning residues (tree stems plus tree crowns) (RM) and retention of thinning residues (crowns retained with stem removal) (RT) treatments. Total soil carbon (TC) and nitrogen (TN) content in the residue retention treatment were significantly greater than in residue removal treatments (p < 0.05). The relative abundance of the dominant soil bacteria phyla were, in descending order: Proteobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Planctomycetes, Gemmatimonadetes, and Bacteroidetes, with a total relative abundance of more than 80%. Acidobacteria were enriched in the RM treatment, while Proteobateria, Actinobacteria and Bacteroidetes were greater in the RT treatment. Rhizobiales and Rhodospirillales (belonging to the α-Proteobacteria) were enriched in the RM treatment. Soil bacteria α diversity was not significantly different among different treatments. Spearman correlation analysis showed that the α diversity index was significantly negatively correlated with TC and TN. Lefse analysis revealed that 42 significant soil bacteria from phylum to genus were found in the two different thinning residue treatments. Redundancy analysis showed that soil TC and TN were the major drivers of variation in soil bacterial community structure. Overall, thinning residue retention increased the availability of resources to the soil bacterial community, thus changing bacterial community structure. This research provides a theoretical basis for the regulation of plantation forest soil fertility and quality.

Changes in the Distribution of Intrauterine Microbiota May Attribute to Immune Imbalance in the CBA/J×DBA/2 Abortion-Prone Mice Model

Background: Female Genital Tract (FGT) is an important micro-ecological area of human body. Microbiota in the lower reproductive tract may subsequently invade the uterine cavity during embryo implantation and produce immune responses. CBA/J×DBA/2 mating combination has been widely used as an abortion-prone mice model but whether microbiota existed in their uterine cavity remains unclear. In this context, the role of the microbial communities in immune response deserves attention.

Objective: To investigate the relationship between the distribution of microbiota in the uterine cavity of CBA/J×DBA/2 abortion-prone mouse model and the immune imbalance of the maternal-fetal interface.

Methods: In this study, female CBA/J mice were paired with male DBA/2 mice to develop an abortion-prone model (BA group), and with male BALB/c mice to build a standard pregnancy model (BC group). The non-pregnant female mice were served as the control group (C group). Uterine flushing fluid and sera were collected on day 13.5 of pregnancy. 16S rRNA sequencing technology was used to analyze the distribution of intrauterine microbiota. Phylogenetic Investigation of Communities were conducted to predict the microbiota functions by Reconstruction of Unobserved States (PICRUST) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The serum IL 10, INF-γ, and TNF-α levels were examined using Enzyme-linked immunosorbent assay (ELISA) method.

Results: All samples were detected with microbial communities. The α diversity (p = 0.00077) had significant differences among three groups. Proteobacteria was the most dominant phylum in C group (mean = 83.21%) and BA group (mean = 43.23%). Firmicutes was dominant in BC group (mean = 46.4%), as well as the second dominant one in C group (mean = 12.63%) and BA group (mean = 40.55%). Microbiota functions were associated with metabolism and immune response through the NOD-like receptor signaling pathway. The serum IL 10 level in BA group were significantly lower than that in BC group (10.14 ± 1.90 pg/ml, n = 8; vs. 19.03 ± 1.82 pg/ml, n = 10; p = 0.004). The serum TNF-α and INF-γ level in BA group were also significantly higher than that in BC group (523.1 ± 58.14 pg/ml, n = 8 vs. 310.3 ± 28.51 pg/ml, n = 10, p = 0.0029; 69.22 ± 5.38 pg/ml, n = 8 vs. 50.85 ± 2.45 pg/ml, n = 10, p = 0.0042).

Conclusion: Microbial communities were colonized in uterine cavity of CBA/J mice both at non-pregnant stage and pregnant stage when mated with both BALB/c and DBA/2 male mice. The differentially abundant microbiome may be attributed to the immune tolerance through binding to the NOD-like receptor.

Smallholder Farmers' Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Simple Summary

Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity.

Abstract

Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.

The Rhizosphere Microbiome of Mikania micrantha Provides Insight Into Adaptation and Invasion

Mikania micrantha is a noxious invasive plant causing enormous economic losses and ecological damage. Soil microbiome plays an important role in the invasion process of M. micrantha, while little is known about its rhizosphere microbiome composition and function. In this study, we identified the distinct rhizosphere microbial communities of M. micrantha, by comparing them with those of two coexisting native plants (Polygonum chinense and Paederia scandens) and the bulk soils, using metagenomics data from field sampling and pot experiment. As a result, the enrichment of phosphorus-solubilizing bacteria Pseudomonas and Enterobacter was consistent with the increased soil available phosphorus in M. micrantha rhizosphere. Furthermore, the pathogens of Fusarium oxysporum and Ralstonia solanacearum and pathogenic genes of type III secretion system (T3SS) were observed to be less abundant in M. micrantha rhizosphere, which might be attributed to the enrichment of biocontrol bacteria Catenulispora, Pseudomonas, and Candidatus Entotheonella and polyketide synthase (PKS) genes involved in synthesizing antibiotics and polyketides to inhibit pathogens. These findings collectively suggested that the enrichment of microbes involved in nutrient acquisition and pathogen suppression in the rhizosphere of M. micrantha largely enhances its adaptation and invasion to various environments.

Biological nitrogen removal and metabolic characteristics in a full-scale two-staged anoxic-oxic (A/O) system to treat optoelectronic wastewater

In order to explore the treatment efficiency of optoelectronic wastewater and pollutant degradation mechanism of full-scale two-stage AO process, 160 d monitoring was conducted in this study. The results showed that the two-stage AO process owned relatively stable nitrogen and organic matter removal performance. The average concentration of COD, NH₄⁺-N, and TN in effluent was 54, 3.78 and 13.77 mg L^-1, respectively, and the removal rate was over 80%. The results of high-throughput sequencing demonstrated that the dominant microorganism was Proteobacteria, Bacteroidetes, Firmicutes, Chlorofeli, and Acidobacteria, and differences of interaction networks exited between aerobic and anoxic units. Meanwhile, the microorganism metabolism in aerobic units was significantly different from that in anoxic unit, and the metabolism of the microbial community for treating optoelectronic wastewater was significantly different from that for treating urban domestic sewage.

Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks

Fusarium Head Blight (FHB) is one of the most devastating diseases of cereals worldwide, threatening both crop production by affecting cereal grain development, and human and animal health by contaminating grains with mycotoxins. Despite that maize residues constitute the primary source of inoculum for Fusarium pathogenic species, the structure and diversity of Fusarium spp. and microbial communities in maize residues have received much less attention than in grains. In this study, a metabarcoding approach was used to study the bacterial, fungal and Fusarium communities encountered in maize stalks collected from 8 fields in Brittany, France, after maize harvest during fall 2015. Some predominant genera found in maize residues were cereal or maize pathogens, such as the fungal Fusarium, Acremonium, and Phoma genera, and the bacterial Pseudomonas and Erwinia genera. Furthermore, a high predominance of genera with previously reported biocontrol activity was found, including the bacterial Sphingomonas, Pedobacter, Flavobacterium, Pseudomonas, and Janthinobacterium genera; and the fungal Epicoccum, Articulospora, Exophiala, and Sarocladium genera. Among Fusarium spp., F. graminearum and F. avenaceum were dominant. We also found that the maize cultivar and previous crop could influence the structure of microbial communities. Using SparCC co-occurrence network analysis, significant negative correlations were obtained between Fusarium spp. responsible for FHB (including F. graminearum and F. avenaceum) and bacterial OTUs classified as Sphingomonas and fungal OTUs classified as Sarocladium and Epicoccum. Considering that isolates belonging to these taxa have already been associated with antagonist effect against different Fusarium spp. and/or other pathogenic microorganisms and due to their predominance and negative associations with Fusarium spp., they may be good candidates as biocontrol agents. Combining the use of Fusarium-specific primers with universal primers for bacteria and fungi allowed us to study the microbial communities, but also to track correlations between Fusarium spp. and other bacterial and fungal genera, using co-occurrence network analysis. Such approach could be a useful tool as part of a screening strategy for novel antagonist candidates against toxigenic Fusarium spp., allowing the selection of taxa of interest.

Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages

Harvest residues contain large stores of carbon (C) and nitrogen (N) in forest plantations. Decomposing residues can release labile C and N into soil and thus provide substrates for soil bacterial communities. Previous studies showed that residue retention could increase soil C and N pools and activate bacterial communities in the short term (≤ 10 years). The current study examined the effects of a long-term (19-year) harvest residue retention on soil total and water and hot water extractable C and N pools, as well as bacterial communities via Illumina MiSeq sequencing. The experiment was established in a randomised complete block design with four replications, southeast Queensland of Australia, including no (R0), single (R1, 51 to 74 t ha^-1 dry matter) and double quantities (R2, 140 t ha^-1 dry matter) of residues retained. Generally, no significant differences existed in total C and N, as well as C and N pools extracted by water and hot water among the three treatments, probably due to negligible amounts of labile C and N released from harvest residues. Soil δ¹⁵N significantly decreased from R0 to R1 to R2, probably due to reduced N leaching with residue retention (P < 0.001). Residue retention increased the relative abundances of Actinobacteria (P = 0.016) and Spartobacteria (P < 0.001), whereas decreased Betaproteobacteria (P = 0.050). This favour for the oligotrophic groups probably caused the decrease in the bacterial diversity as revealed by Shannon index (P = 0.025). Hence, our study suggests that residue retention is not an appropriate management practice in the long term.

Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil

Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha^-1 when its ratio of NH₄⁺/NO₃^--N (R_N) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha^-1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R_N (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha^-1) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R_N significantly reduced soil bacterial alpha diversity (p<0.05) and altered bacterial community structure (e.g., the relative abundances of genera Dyella and Rhodoblastus affiliated to Proteobacteria increased). Redundancy analysis demonstrated that ADN flux and R_N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil.

Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil

Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate^_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage

Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar (Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar (G. barbadense L.) by high-throughput sequencing technology. Six bacterial phyla were found dominantly in cotton rhizosphere bacterial community including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. The abundance of Acidobacteria, Cyanobacteria, Firmicutes, Planctomycetes and Proteobacteria were largely influenced by cotton root. Bacterial α-diversity in rhizosphere was lower than that of bulk soil in nutrient-rich soil, but higher in cotton continuous cropping field soil. The β-diversity in nutrient-rich soil was greater than that in continuous cropping field soil. The community structure of the rhizosphere bacteria varied significantly during different developmental stages. Our results provided insights into the dynamics of cotton rhizosphere bacterial community and would facilitate to improve cotton growth and development through adjusting soil bacterial community structure artificially.