Endophytic Aspergillii and Penicillii from medicinal plants: a focus on antimicrobial and multidrug resistant pathogens inhibitory activity.

The rise of multidrug resistance among microorganisms, where they develop resistance against formerly efficacious drugs, has led to increased disease prevalence and mortality rates, posing a growing challenge. Globally, antibiotic resistance has made a significant impact, causing millions of fatalities each year. Endophytic fungi have gained considerable attention in research due to their potential to produce a wide variety of secondary metabolites, including natural substances with antimicrobial capabilities. The genera Aspergillus and Penicillium stand out as the most prevalent species of endophytic fungi. Filamentous fungi, such as these are responsible for the production of 45% of known microbial metabolites. This review focuses on exploring the bioactive substances produced by endophytic fungi from these two genera, particularly in conjunction with medicinal plants. Emphasis is placed on their antimicrobial activity and their ability to inhibit multidrug-resistant pathogens. As the need for alternative treatments to combat drug-resistant infections continues to grow, endophytic fungi have the potential to provide a valuable source of bioactive molecules for medical applications.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid.

Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.

Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths.

The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.

From desertification to restoration in the Brazilian semiarid region: Unveiling the potential of land restoration on soil microbial properties.

Land desertification poses a significant challenge in the Brazilian semiarid region, encompassing a substantial portion of the country. Within this region, the detrimental effects of human activities, particularly unsuitable anthropic actions, have resulted in diminished vegetation cover and an accelerated rate of soil erosion. Notably, practices such as overgrazing and the conversion of native forests into pasturelands have played a pivotal role in exacerbating the process of land desertification. Ultimately, land desertification results in significant losses of soil organic matter and microbial diversity. To address this pressing issue and contribute to the existing literature, various land restoration practices, such as grazing exclusion, cover crops, and terracing, have been implemented in the Brazilian semiarid. These practices have shown promising results in terms of enhancing soil fertility and restoring microbial properties. Nonetheless, their effectiveness in improving soil microbial properties in the Brazilian semiarid region remains a subject of ongoing study. Recent advances in molecular techniques have improved our understanding of microbial communities in lands undergoing desertification and restoration. In this review, we focus on assessing the effectiveness of these restoration practices in revitalizing soil microbial properties, with a particular emphasis on the soil microbiome and its functions. Through a critical assessment of the impact of these practices on soil microbial properties, our research aims to provide valuable insights that can help mitigate the adverse effects of desertification and promote sustainable development in this ecologically sensitive region.

Draft genome sequences of representative Paenibacillus polymyxa, Bacillus cereus, Fictibacillus sp., and Brevibacillus agri strains isolated from Amazonian dark earth.

Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as Paenibacillus polymyxa, while the remaining four were unique representatives of Paenibacillus vini, Bacillus cereus, Brevibacillus agri, and Fictibacillus sp., respectively. Each strain exhibited antagonistic activity against Fusarium oxysporum, underscoring their potential as sustainable agriculture resources.

Soil and foliar Si fertilization alters elemental stoichiometry and increases yield of sugarcane cultivars.

Silicon (Si) fertilization is widely recognized to improve the development of crops, especially in tropical soils and cultivation under dryland management. Herein, our working hypothesis was that Si stoichiometry favors the efficient use of carbon (C), nitrogen (N), and phosphorus (P) in sugarcane plants. Therefore, a field experiment was carried out using a 3 × 3 factorial scheme consisting of three cultivars (RB92579, RB021754 and RB036066) and three forms of Si application (control without Si; sodium silicate spray at 40 mmol L-1 in soil during planting; sodium silicate spray at 40 mmol L-1 on leaves at 75 days after emergence). All Si fertilizations altered the elemental C and P stoichiometry and sugarcane yield, but silicon-induced responses varied depending on sugarcane cultivar and application method. The most prominent impacts were found in the leaf Si-sprayed RB92579 cultivar, with a significant increase of 7.0% (11 Mg ha-1) in stalk yield, 9.0% (12 Mg ha-1) in total recoverable sugar, and 20% (4 Mg ha-1) in sugar yield compared to the Si-without control. In conclusion, our findings clearly show that silicon soil and foliar fertilization alter C:N:P stoichiometry by enhancing the efficiency of carbon and phosphorus utilization, leading to improved sugarcane production and industrial quality.

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.

BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Linking above and belowground carbon sequestration, soil organic matter properties, and soil health in Brazilian Atlantic Forest restoration.

Forest restoration mitigates climate change by removing CO2 and storing C in terrestrial ecosystems. However, incomplete information on C storage in restored tropical forests often fails to capture the ecosystem's holistic C dynamics. This study provides an integrated assessment of C storage in above to belowground subsystems, its consequences for greenhouse gas (GHG) fluxes, and the quantity, quality, and origin of soil organic matter (SOM) in restored Atlantic forests in Brazil. Relations between SOM properties and soil health indicators were also explored. We examined two restorations using tree planting ('active restoration'): an 8-year-old forest with green manure and native trees planted in two rounds, and a 15-year-old forest with native-planted trees in one round without green manure. Restorations were compared to reformed pasture and primary forest sites. We measured C storage in soil layers (0-10, 10-20, and 20-30 cm), litter, and plants. GHG emissions were assessed using CH4 and CO2 fluxes. SOM quantity was evaluated using C and N, quality using humification index (HLIFS), and origin using δ13C and δ15N. Nine soil health indicators were interrelated with SOM attributes. The primary forest presented the highest C stocks (107.7 Mg C ha-1), followed by 15- and 8-year-old restorations and pasture with 69.8, 55.5, and 41.8 Mg C ha-1, respectively. Soil C stocks from restorations and pasture were 20% lower than primary forest. However, 8- and 15-year-old restorations stored 12.3 and 28.3 Mg ha-1 more aboveground C than pasture. The younger forest had δ13C and δ15N values of 2.1 and 1.7‰, respectively, lower than the 15-year-old forest, indicating more C derived from C3 plants and biological N fixation. Both restorations and pasture had at least 34% higher HLIFS in deeper soil layers (10-30 cm) than primary forest, indicating a lack of labile SOM. Native and 15-year-old forests exhibited higher soil methane influx (141.1 and 61.9 µg m-2 h-1). Forests outperformed pasture in most soil health indicators, with 69% of their variance explained by SOM properties. However, SOM quantity and quality regeneration in both restorations approached the pristine forest state only in the top 10 cm layer, while deeper soil retained agricultural degradation legacies. In conclusion, active restoration of the Atlantic Forest is a superior approach compared to pasture reform for GHG mitigation. Nonetheless, the development of restoration techniques to facilitate labile C input into deeper soil layers (>10 cm) is needed to further improve soil multifunctionality and long-term C storage.

Exploring the diversity and composition of soil microbial communities in different soybean-maize management systems.

Soybean-maize are cultivated in different management systems, such as no-tillage and pastures, which presents potential to add organic residues, and it can potentially impacts the soil microbial community present in these systems. Thus, this study aimed to examine the effects of different soybean-maize management practices on the diversity and composition of soil microbial communities. Specifically, 16 S rRNA amplicon sequencing was used to investigate whether the use of pasture species in a fallowing system influences microbial communities in a soybean-maize rotation system, as compared to conventional tillage and no-tillage systems. The results indicate that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems leads to distinct responses within the soil microbial community. It was found that different soybean-maize management systems, particularly those with U. brizantha, affected the microbial community, likely due to the management applied to this pasture species. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness (∼2000 operational taxonomic units) and diversity index (∼6.0). Proteobacteria (∼30%), Acidobacteria (∼15%), and Verrucomicrobia (∼10%) were found to be the most abundant phyla in the soil under tropical native vegetation, while soils under cropland had an increased abundance of Firmicutes (∼30% to ∼50%) and Actinobacteria (∼30% to ∼35%). To summarize, this study identified the impacts of various soybean-maize management practices on the soil microbial community and emphasized the advantages of adding U. brizantha as a fallow species.

Forest restoration rehabilitates soil multifunctionality in riparian zones of sugarcane production landscapes.

Brazilian sugarcane plays a vital role in the production of both sugar and renewable energy. However, land use change and long-term conventional sugarcane cultivation have degraded entire watersheds, including a substantial loss of soil multifunctionality. In our study, riparian zones have been reforested to mitigate these impacts, protect aquatic ecosystems, and restore ecological corridors within the sugarcane production landscapes. We examined (i) how forest restoration enables rehabilitation of the soil's multifunctionality after long-term sugarcane cultivation and (ii) how long it takes to regain ecosystem functions comparable to those of a primary forest. We investigated a time series of riparian forests at 6, 15, and 30 years after starting restoration by planting trees (named 'active restoration') and determined soil C stocks, δ13C (indicative of C origin), as well as measures indicative of soil health. A primary forest and a long-term sugarcane field were used as references. Eleven soil physical, chemical, and biological indicators were used for a structured soil health assessment, calculating index scores based on soil functions. Forest-to-cane conversion reduced 30.6 Mg ha-1 of soil C stocks, causing soil compaction and loss of cation exchange capacity, thus degrading soil's physical, chemical, and biological functions. Forest restoration for 6-30 years recovered 16-20 Mg C ha-1 stored in soils. In all restored sites, soil functions such as supporting root growth, aerating the soil, nutrient storage capacity, and providing C energy for microbial activity were gradually recovered. Thirty years of active restoration was sufficient to reach the primary forest state in overall soil health index, multifunctional performance, and C sequestration. We conclude that active forest restoration in sugarcane-dominated landscapes is an effective way to restore soil multifunctionality approaching the level of the native forest in approximately three decades. Moreover, the C sequestration in the restored forest soils will help to mediate global warming.

Short-term responses of plant growth-promoting bacterial community to the herbicides imazethapyr and flumioxazin.

Imazethapyr and flumioxazin are widely recommended herbicides for soybean fields due to their broad-spectrum effects. However, although both herbicides present low persistence, their potential impact on the community of plant growth-promoting bacteria (PGPB) is unclear. To address this gap, this study assessed the short-term effect of imazethapyr, flumioxazin, and their mixture on the PGPB community. Soil samples from soybean fields were treated with these herbicides and incubated for 60 days. We extracted soil DNA at 0, 15, 30, and 60 days and sequenced the 16S rRNA gene. In general, the herbicides presented temporary and short-term effects on PGPB. The relative abundance of Bradyrhizobium increased, while Sphingomonas decreased on the 30th day with the application of all herbicides. Both herbicides increased the potential function of nitrogen fixation at 15th days and decreased at 30th and 60th days of incubation. The proportions of generalists were similar (∼42%) comparing each herbicide and the control, while the proportion of specialists increased (varying from 24.9% to 27.6%) with the application of herbicides. Imazethapyr, flumioxazin and their mixture did not change the complexity and interactions of the PGPB network. In conclusion, this study showed that, in the short term, the application of imazethapyr, flumioxazin, and their mixture, at the recommended field rates, does not negatively affect the community of plant growth-promoting bacteria.

Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Physicochemical and bacterial changes during composting of vegetable and animal-derived agro-industrial wastes.

This study investigates the impact of different agro-industrial organic wastes (i.e., sugarcane filter cake, poultry litter, and chicken manure) on the bacterial community and their relationship with physicochemical attributes during composting. Integrative analysis was performed by combining high-throughput sequencing and environmental data to decipher changes in the waste microbiome. The results revealed that animal-derived compost stabilized more carbon and mineralized a more organic nitrogen than vegetable-derived compost. Composting enhanced bacterial diversity and turned the bacterial community structure similar among all wastes, reducing Firmicutes abundance in animal-derived wastes. Potential biomarkers indicating compost maturation were Proteobacteria and Bacteroidota phyla, Chryseolinea genus and Rhizobiales order. The waste source influenced the final physicochemical attributes, whereas composting enhanced the complexity of the microbial community in the order of poultry litter > filter cake > chicken manure. Therefore, composted wastes, mainly the animal-derived ones, seem to present more sustainable attributes for agricultural use, despite their losses of C, N, and S.

Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.

Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.

Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid.

Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.

Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil.

Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.

Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination.

Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg-1 Cr) and Cr-contaminated soils (∼250 mg kg-1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.

Applications of Cr-rich composted tannery sludge in the soil decrease microbial biomass and select specific bacterial groups.

The tannery industries generate a solid waste known as tannery sludge, which is composed of organic and inorganic compounds, mainly chromium (Cr). When Cr is not removed from the tannery sludge, this solid waste is metal-rich and its application could affect the soil microorganisms. Alternatively, the composting of the tannery sludge can contribute to decreasing the concentration of Cr in the composted tannery sludge (CTS). However, in some cases, the concentration of Cr remains high in the CTS. During the last 10 years, the Cr-rich CTS has been successively applied in the soil, and its effect on soil microbial properties was verified. Here, we discuss the effect of successive applications of Cr-rich CTS on soil microbes. Interestingly, the findings have shown that successive applications of Cr-rich CTS selected specific soil microbial groups with potential functions. In addition, the studies added a new focus to further research evaluating the potential effect of successive applications of Cr-rich CTS on the rare microbial community.

Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants.

Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.