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.

Draft genome sequences of 13 putatively novel Haemophilus species and strains assembled from human saliva.

We present the draft metagenome-assembled genomes (MAGs) of 13 Haemophilus representatives from human saliva. MAGs were reconstructed by a streamlined pre-assembly mapping approach performed against 9 clinically relevant reference genomes. Overall, genomes belonging to 2 potentially novel Haemophilus species and 11 strains were recovered, as determined by genome-wide ANI analysis.

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.

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.

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.

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.

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.

Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems.

Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH4 cycling microbial communities in soils sampled during hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH4 emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH4 fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH4 fluxes in RBSs in order to maximize RBS environmental benefits.

Ecological co-occurrence and soil physicochemical factors drive the archaeal community in Amazonian soils.

We evaluated the co-occurrence of archaeal taxonomic groups and soil physicochemical characteristics in relation to the structuring of the archaeal community in Amazonian soil under different land use systems. Soil samples were collected in primary forest (PF), secondary forest (SF), agricultural systems (AG) and cattle pastures (PA). Archaeal community composition was revealed based on high-throughput amplicon sequencing of the 16S rRNA gene. The results revealed co-occurrence of archaeal classes, with two groups formed: Thaumarchaeota classes, including South Africa Gold Mine-Group 1 (SAGMG-1), Crenarchaeotic group (SCG) and Crenarchaeota candidate division YNPFFA, with predominance in PF and SF; and Bathyarchaeota_unclassified, Methanomicrobia and Methanobacteria (Euryarchaeota) with the FHMa11 terrestrial group, with predominance in PA. The number of co-occurrences between groups was lower in SF, AG and PA (approximately 30%) than in PF. The qPCR analysis revealed that PF also had the largest number of archaeal representatives. Soil texture may be a limiting factor of interactions between groups since the most representative groups, SAGMG-1 and the SCG (over 20% in all sites), were positively associated with coarse sand, the soil factor most correlated with the groups (33% of the total). These results suggest that interactions between archaeal classes belonging to different phyla may be dependent on the number of individuals in the soil environment. In this context, differences in soil physical structure among the land use systems can reduce the representatives of key groups and consequently the co-occurrence of Archaea, which could compromise the natural dynamics of this complex environment.

Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.

Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change.

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world's largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome.

We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.

Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere.

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.

The effect of Haemonchus contortus and Trichostrongylus colubriforms infection on the ruminal microbiome of lambs.

We evaluated Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC) infection on the ruminal microbial community of Santa Ines lambs to better understand the pathophysiology of parasite infections and the interactions among gastrointestinal nematodes and gut resident microbiota. In this study, 18 six months of age lambs were maintained for 34 days in individual pens divided into three treatments that included animals infected with HC and TC, and control (infection-free). Haematological, ruminal parameter and microbial nitrogen absorbed by pune derivatives, as well as enteric methane emission (CH4), were analysed, and the rumen microbial taxonomic and functional profile assessed by shotgun metagenomics. The analysis showed that total protein, albumin, urea, and butyrate level were lower in animals infected by both parasites, while HC infection also decreased the haemoglobin level. Both infected groups (TC and HC) increased the enteric methane emission (CH4). TC and HC infections increased the diversity and richness of functional microbial genes. Most alterations in the rumen microbiome composition of infected groups are associated with the suppression of microbes involved in microbial homeostasis maintenance and expansion of the archaeal community in the infected animals. Infection led to an increased abundance of nitrogen, amino acid, protein, and energy metabolism genes. Overall, TC and HC infection increased the enteric methane emission, negatively affected taxon's responsible for maintenance de rumen homeostasis and modulated some important genes related to protein and energy metabolism.

Ovarian activation delays in peripubertal ewe lambs infected with Haemonchus contortus can be avoided by supplementing protein in their diets.

BACKGROUND: The ewe lamb nutritional and physiological state interfere with the ovarian environment and fertility. The lack or excess of circulating nutrients reaching the ovary can change its gene expression. A protein deficiency in the blood caused by an Haemonchus contortus abomasal infection is detrimental to the organism's development during puberty. The peripubertal period is a time of intensive growth that requires a high level of nutrients. An essential feature controlling pubertal arousal and female reproductive potential is ovarian follicle growth activation. Protein supplementation improves the sheep's immune response to helminthic infections. We aimed to determine if supplementing protein in infected ewe lambs' diet would impact the ovarian environment leading to earlier ovarian follicle activation than in infected not supplemented animals. METHODS: We fed 18 Santa Ines ewe lambs (Ovis aries) - bred by the same ram - with either 12% protein (Control groups) or 19% protein (Supplemented groups) in their diets. After 35 days of the diet, they were each artificially infected or not with 10,000 Haemonchus contortus L3 larvae. Following 77 days of the diet and 42 days of infection, we surgically collected their left ovaries and examined their genes expression through RNA sequencing. RESULTS: We found that protein supplementation in infected animals led to an up-regulation of genes (FDR p-values < 0.05) and biological processes (p-value cut-off = 0.01) linked to meiotic activation in pre-ovulatory follicles and primordial follicle activation, among others. The supplemented not infected animals also up-regulated genes and processes linked to meiosis and others, such as circadian behaviour. The not supplemented animals had these same processes down-regulated while up-regulated processes related to tissue morphogenesis, inflammation and immune response. CONCLUSION: Diet's protein supplementation of peripubertal infected animals allowed them to express genes related to a more mature ovarian follicle stage than their half-sisters that were not supplemented. These results could be modelling potential effects of the interaction between environmental factors, nutrition and infection on reproductive health. When ovarian activation is achieved in a timely fashion, the ewe may generate more lambs during its reproductive life, increasing sheep breeders' productivity.

Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production.

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.

Soil CO2 emission and soil attributes associated with the microbiota of a sugarcane area in southern Brazil.

The spatial structure of soil CO2 emission (FCO2) and soil attributes are affected by different factors in a highly complex way. In this context, this study aimed to characterize the spatial variability patterns of FCO2 and soil physical, chemical, and microbiological attributes in a sugarcane field area after reform activities. The study was conducted in an Oxisol with the measurement of FCO2, soil temperature (Ts), and soil moisture (Ms) in a regular 90 × 90-m grid with 100 sampling points. Soil samples were collected at each sampling point at a depth of 0-0.20 m to determine soil physical (density, macroporosity, and microporosity), particle size (sand, silt, and clay), and chemical attributes (soil organic matter, pH, P, K, Ca, Mg, Al, H + Al, cation exchange capacity, and base saturation). Geostatistical analyses were performed to assess the spatial variability and map soil attributes. Two regions (R1 and R2) with contrasting emission values were identified after mapping FCO2. The abundance of bacterial 16S rRNA, pmoA, and nifH genes, determined by real-time quantitative PCR (qPCR), enzymatic activity (dehydrogenase, urease, cellulase, and amylase), and microbial biomass carbon were determined in R1 and R2. The mean values of FCO2 (2.91 µmol m-2 s-1), Ts (22.6 °C), and Ms (16.9%) over the 28-day period were similar to those observed in studies also conducted under Oxisols in sugarcane areas and conventional soil tillage. The spatial pattern of FCO2 was similar to that of macropores, air-filled pore space, silt content, soil organic matter, and soil carbon decay constant. No significant difference was observed between R1 and R2 for the copy number of bacterial 16S rRNA and nifH genes, but the results of qPCR for the pmoA gene presented differences (p < 0.01) between regions. The region R1, with the highest FCO2 (2.9 to 4.2 µmol m-2 s-1), showed higher enzymatic activity of dehydrogenase (33.02 µg TPF g-1 dry soil 24 h-1), urease (41.15 µg NH4-N g-1 dry soil 3 h-1), amylase (73.84 µg glucose g-1 dry soil 24 h-1), and microbial biomass carbon (41.35 µg C g-1 soil) than R2, which had the lowest emission (1.9 to 2.7 µmol m-2 s-1). In addition, the soil C/N ratio was higher in R2 (15.43) than in R1 (12.18). The spatial pattern of FCO2 in R1 and R2 may not be directly related to the total amount of the microbial community (bacterial 16S rRNA) in the soil but to the specific function that these microorganisms play regarding soil carbon degradation (pmoA).

Sorption-desorption and biodegradation of sulfometuron-methyl and its effects on the bacterial communities in Amazonian soils amended with aged biochar.

Sulfometuron-methyl is a broad-spectrum herbicide, used throughout Brazil; however, its environmental impacts in biochar (BC) amended soils is not fully understood. Biochar is known to enhance soil quality but can also have undesired effects such as altering the bioavailability and behavior of herbicides. Microbial communities can degrade herbicides such as sulfometuron-methyl in soils; however, they are known to be affected by BC. Therefore, it is important to understand the tripartite interaction between these factors. This research aimed to evaluate the sorption-desorption and biodegradation of sulfometuron-methyl in Amazonian soils amended with BC, and to assess the effects of the interactions between BC and sulfometuron-methyl on soil bacterial communities. Soil samples were collected from field plots amended with BC at three doses (0, 40 and 80 t ha-1) applied ten years ago. The herbicide sorption and desorption were evaluated using a batch equilibrium method. Mineralization and biodegradation studies were conducted in microcosms incubated with 14C-sulfometuron-methyl for 80 days. Systematic soil sampling, followed by DNA extraction, quantification (qPCR) and 16S rRNA amplicon sequencing were performed. The presence of BC increased the sorption of the herbicide to the soil by 11% (BC40) and 16% (BC80) compared to unamended soil. The presence of BC also affected the degradation of 14C-sulfometuron-methyl, reducing the mineralization rate and increasing the degradation half-life times (DT50) from 36.67 days in unamended soil to 52.11 and 55.45 days in BC40 and BC80 soils, respectively. The herbicide application altered the bacterial communities, affecting abundance and richness, and changing the taxonomic diversity (i.e., some taxa were promoted and other inhibited). A tripartite interaction was found between BC, the herbicide and soil bacterial communities, suggesting that it is important to consider the environmental impact of soil applied herbicides in biochar amended soils.

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon.

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.