Microbial metabolic activity in Amazon floodplain forest and agricultural soils.

Microorganisms play an essential role in ecosystem functions. An increasingly used method for conducting functional analyses of a soil microbial community is based on the physiological profile at the community level. This method allows the metabolic capacity of microorganisms to be assessed based on patterns of carbon consumption and derived indices. In the present study, the functional diversity of microbial communities was assessed in soils from seasonally flooded-forest (FOR) and -traditional farming systems (TFS) in Amazonian floodplains flooded with black, clear, and white water. The soils of the Amazon floodplains showed differences in the metabolic activity of their microbial communities, with a general trend in activity level of clear water floodplain > black water floodplain > white water floodplain. The redundancy analysis (RDA) indicated that soil moisture (flood pulse) was the most important environmental parameter in determining the metabolic activity of the soil microbial communities in the black, clear, and white floodplains. In addition, the variance partitioning analysis (VPA) indicated that the microbial metabolic activity of the soil was more influenced by water type (41.72%) than by seasonality (19.55%) and land use type (15.28%). The soil microbiota of the white water floodplain was different from that of the clear water and black water floodplains in terms of metabolic richness, as the white water floodplain was mainly influenced by the low substrate use during the non-flooded period. Taken together, the results show the importance of considering soils under the influence of flood pulses, water types, and land use as environmental factors when recognizing functional diversity and ecosystem functioning in Amazonian floodplains.

Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia.

Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.

Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments.

Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities.

Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 -), which can be further oxidized to nitrate (NO3 -). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 - and NO3 -, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 +) and NO3 --and NO2 --dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.

Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons.

Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.

Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils.

Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.

Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon.

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.

Assessment of microbial diversity associated with CH4 emission from sugarcane vinasse storage and transportation systems.

Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH4) emission during storage and transportation stages. Considering that CH4 emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH4 patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH4 emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH4 production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 107 and 4.3 × 1010) and subsequent positive correlation with CH4 emissions (R2 = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH4 emissions, thereby making bioethanol a greener biofuel.

Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations.

Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC1S4) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from -164 to 277 kg ha-1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from drought-stressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression.

Gestational and lactational exposure to gossypol alters the testis transcriptome.

BACKGROUND: Reproductive capacity can be altered by challenges experienced during critical periods of development, including fetal development and early neonatal life. Gossypol is a polyphenolic compound, commonly found in cotton seeds, that impairs male reproduction. Here, we investigated whether the exposure to gossypol in utero and during lactation alters male reproductive function in sheep. From conception until 60 days postpartum, ewes were randomly assigned to a control diet or a gossypol-rich diet based on cottonseed. Lamb testicles were removed at 60 days of age and subjected to RNA-sequencing. RESULTS: Lambs derived from the maternal cottonseed diet showed significantly lower growth and lower testis weight as a proportion of the total body weight, and reduced testosterone levels. In addition, the testis transcriptome was significantly altered by the maternal cottonseed diet. Most of the altered genes are directly implicated in testis development and sperm biology, cell communication, iron ion metabolism, calcium homeostasis and signaling, among other functions. Interestingly, network analysis revealed that exposure to gossypol significantly disturbed coexpression patterns among spermatogenesis-related genes, suggesting a disruption in coregulation mechanisms. CONCLUSIONS: Our findings provide evidence that maternal exposure to gossypol alters male reproductive function in the offspring, with potential lasting or lifelong negative consequences.

A new glance on root-to-shoot in vivo zinc transport and time-dependent physiological effects of ZnSO4 and ZnO nanoparticles on plants.

Understanding nanoparticle root uptake and root-to-shoot transport might contribute to the use of nanotechnology in plant nutrition. This study performed time resolved experiments to probe Zn uptake, biotransformation and physiological effects on Phaseolus vulgaris (L.). Plants roots were exposed to ZnO nanoparticles (40 and 300 nm) dispersions and ZnSO4(aq) (100 and 1000 mg Zn L-1) for 48 h. Near edge X-ray absorption spectroscopy showed that 40 nm ZnO was more easily dissolved by roots than 300 nm ZnO. It also showed that in the leaves Zn was found as a mixture Zn3(PO4)2 and Zn-histidine complex. X-ray fluorescence spectroscopy showed that root-to-shoot Zn-translocation presented a decreasing gradient of concentration and velocity, it seems radial Zn movement occurs simultaneously to the axial xylem transport. Below 100 mg Zn L-1, the lower stem tissue section served as a buffer preventing Zn from reaching the leaves. Conversely, it was not observed for 1000 mg Zn L-1 ZnSO4(aq). Transcriptional analysis of genes encoding metal carriers indicated higher expression levels of tonoplast-localized transporters, suggesting that the mechanism trend to accumulate Zn in the lower tissues may be associated with an enhanced of Zn compartmentalization in vacuoles. The photosynthetic rate, transpiration, and water conductance were impaired by treatments.

Effect of drought stress on the genetic architecture of photosynthate allocation and remobilization in pods of common bean (Phaseolus vulgaris L.), a key species for food security.

BACKGROUND: Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed quality. Previous studies have shown that photosynthate remobilization and partitioning is one of the main mechanisms of drought tolerance and overall productivity in common bean. RESULTS: In this study, we sought to determine the inheritance of pod harvest index (PHI), a measure of the partitioning of pod biomass to seed biomass, relative to that of grain yield. We evaluated a recombinant inbred population of the cross of ICA Bunsi and SXB405, both from the Mesoamerican gene pool, to determine the effects of intermittent and terminal drought stresses on the genetic architecture of photosynthate allocation and remobilization in pods of common bean. The population was grown for two seasons, under well-watered conditions and terminal and intermittent drought stress in one year, and well-watered conditions and terminal drought stress in the second year. There was a significant effect of the water regime and year on all the traits, at both the phenotypic and QTL levels. We found nine QTLs for pod harvest index, including a major (17% of variation explained), stable QTL on linkage group Pv07. We also found eight QTLs for yield, three of which clustered with PHI QTLs, underscoring the importance of photosynthate remobilization in productivity. We also found evidence for substantial epistasis, explaining a considerable part of the variation for yield and PHI. CONCLUSION: Our results highlight the genetic relationship between PHI and yield and confirm the role of PHI in selection of both additive and epistatic effects controlling drought tolerance. These results are a key component to strengthen the robustness of common bean against drought stresses.

Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.).

BACKGROUND: Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS: An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS: Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS: The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean.

Arbuscular mycorrhizal fungi (AMF) colonization in plants promotes both local and systemic changes in the gene expression profiles of the host that might be relevant for drought-stress perception and response. Drought-tolerant common bean plants (cv. BAT 477), colonized by a mixture of AMF (Glomus clarum, Acaulospora scrobiculata, and Gigaspora rosea), were exposed to a water deprivation regime of 96 h during pre-flowering. Root transcriptomes were accessed through RNA-Seq revealing a set of 9,965 transcripts with significant differential regulation in inoculated plants during a water deficit event, and 10,569 in non-inoculated. These data include 1,589 transcripts that are exclusively regulated by AMF-inoculation, and 2,313 under non-inoculation conditions. Relative gene expression analyses of nine aquaporin-related transcripts were performed in roots and leaves of plants harvested at initial stages of treatment. Significant shifts in gene expression were detected in AM water deficit-treated roots, in relation to non-inoculated, between 48 and 72 h. Leaves also showed significant mycorrhizal influence in gene expression, especially after 96 h. Root cortical cells, harboring or not arbuscules, were collected from both inoculation treatments through a laser microdissection-based technique. This allowed the identification of transcripts, such as the aquaporin PvPIP2;3 and Glucan 1,3 ß-Glucosidase, that are unique to arbuscule-containing cells. During the water deficit treatment, AMF colonization exerted a fine-tune regulation in the expression of genes in the host. That seemed to initiate in arbuscule-containing cells and, as the stressful condition persisted, propagated to the whole-plant through secondary signaling events. Collectively, these results demonstrate that arbuscular mycorrhization leads to shifts in common bean's transcriptome that could potentially impact its adaptation capacity during water deficit events.

Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles.

Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database. We found that the abundance of open read frames (ORFs) annotated as ARGs changed significantly across 43 different families (p-value < 0.05). Co-occurrence network analysis revealed distinct patterns of interactions among ARGs, suggesting that nutrient amendment to soil microbial communities can impact on the coevolutionary dynamics of indigenous ARGs within soil resistome.

Disentangling the influence of earthworms in sugarcane rhizosphere.

For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW-, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW- treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW- rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated.

Oxidative mitigation of aquatic methane emissions in large Amazonian rivers.

The flux of methane (CH4 ) from inland waters to the atmosphere has a profound impact on global atmospheric greenhouse gas (GHG) levels, and yet, strikingly little is known about the dynamics controlling sources and sinks of CH4 in the aquatic setting. Here, we examine the cycling and flux of CH4 in six large rivers in the Amazon basin, including the Amazon River. Based on stable isotopic mass balances of CH4 , inputs and outputs to the water column were estimated. We determined that ecosystem methane oxidation (MOX) reduced the diffusive flux of CH4 by approximately 28-96% and varied depending on hydrologic regime and general geochemical characteristics of tributaries of the Amazon River. For example, the relative amount of MOX was maximal during high water in black and white water rivers and minimal in clear water rivers during low water. The abundance of genetic markers for methane-oxidizing bacteria (pmoA) was positively correlated with enhanced signals of oxidation, providing independent support for the detected MOX patterns. The results indicate that MOX in large Amazonian rivers can consume from 0.45 to 2.07 Tg CH4 yr(-1) , representing up to 7% of the estimated global soil sink. Nevertheless, climate change and changes in hydrology, for example, due to construction of dams, can alter this balance, influencing CH4 emissions to atmosphere.

Soil microbiome responses to the short-term effects of Amazonian deforestation.

Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.