Nitrogen fertilizer management is an important agricultural tool that must be optimized to promote sustainable practices since the nitrogen-fertilizer recovery by plants (NRP) is low, leading to nitrogen losses to the environment. In sugarcane, N-fertilization has been investigated over the years but little attention has been given to N-fertilizer application methods. Sugarcane crop production and environmental impact regarding N-fertilizer application methods (i.e., applied onto the sugarcane straw layer and incorporated into the soil) were investigated in the present study aiming to achieve an environmental-friendly cropping system. Sugarcane yield and NRP, N2O emissions, relevant components of the soil microbiological community and N-fertilizer retention in soil layers were quantified. The experiment was carried out in field conditions where N-fertilizer application methods using 15N-labelled ammonium nitrate (15NH415NO3) were compared to a control treatment with no N-fertilization. Incorporation of N-fertilizer into the soil increased the sugarcane yield by 17

There is evidence that forage grasses such as Megathyrsus and Urochloa can suppress nitrification, with direct or indirect consequences on soil inorganic N dynamics and nitrous oxide (N2O) emissions. However, the influence of soil chemical properties on the dynamics of functional N-genes and losses of N in maize (Zea mays L.) inter cropped with forage grasses under N fertilization is poorly understood. In this study, soil samples and N2O emissions were analyzed from a field experiment in which maize (fertilized or not with ammonium-based fertilizer) was intercropped with Guinea grass (M. maximus cv. Tanzania), palisade grass (U. brizantha cv. Marandu), and ruzigrass (U. ruziziensis cv. Comum). Soil N-cycle microorganisms [16S rRNA of bacteria and archaea, nifH (gene encoding N2-fixing bacteria), ammonia-oxidizing bacteria (AOB) and archaea (AOA), nirS (encoding nitrite reductase), and nosZ (encoding nitrous oxide reductase)] were influenced by forage grass, N fertilization, and sampling time, but no evidence of biological nitrification inhibition was found. Palisade grass was associated with a higher abundance of nifH (7.0 x 105 gene copies g-1 soil, on average) in the absence of N compared with the other grasses (4.3 x 105 gene copies g-1 soil, on average). Nitrogen fertilization increased the abundance of AOB but not AOA. Furthermore, N2O flux was influenced by AOB, water-filled pore space, and N fertilization, whereas the cumulative N2O emission and fertilizer-induced emission factor (0.36%, on average) were not affected by the grasses. In conclusion, this study reveals the strong dominance of AOB under ammonium supply, potentially stimulating N2O emissions in maize-forage grass intercropping systems.

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.

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.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH 4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH 4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH 4 cycling microbial communities and further investigated their responses to seasonal changes. 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 methanogenic (methyl coenzyme-M reductase – mcr A) and methanotrophic (particulate methane monooxygenase – pmo A) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH 4 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. The results presented may contribute to the understanding of the current state of CH 4 cycling in this region.

Growing global demand for bioenergies has raised the interest in using sugarcane crop residues (straw) as feedstock to produce cellulosic ethanol and/or bioelectricity in Brazil. However, indiscriminate straw removal may deplete soil quality, particularly induced by its negative effects on soil microbial communities. A 2-year field study was conducted in soils classified as Oxisol (site 1) and Ultisol (site 2) in southeastern Brazil. The experiment started after plant cane cycle, establishing three straw removal rates (treatments), as follows: total removal, moderated removal, and no removal of sugarcane straw from the field. The amount of straw left on the soil surface and removed in the treatments varied according to the straw yield of each year and location. Soil samples were collected at 0–5- and 5–10-cm layers. The total abundance of bacteria, archaea, and fungi were analyzed by real-time quantitative polymerase chain reaction (qPCR). Bulk density, pH, base saturation, cation exchange capacity, phosphorus (P), and total organic C and soil microbial biomass C (MBC) were also measured. The soil chemical results indicate that the Oxisol presents higher inherent soil fertility compared with the Ultisol. In the first year, the straw had a different significant effect for bacterial and archaeal abundance in both soils and for fungi in the Oxisol site. In the second year, the numbers of gene copies of bacteria, archaea, and fungi in the 0–5-cm layer were higher under moderated and no removal when compared with those under total removal, regardless of site. The MBC decreased significantly under total removal of straw at the Ultisol site. Moderate straw removal has no significant effect on the abundance of soil microbes, but total straw removal may induce sharp reductions (from 23 to 54%) on microbial abundance. Soil microbes are a sensitive indicator to assess soil changes induced by crop residue management and should be taken into account for defining sugarcane straw management towards a sustainable bioenergy production.

The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.

Sugarcane (Saccharum officinarum) residue (straw) has been identified as a promising feedstock for bioenergy production, but excessive straw removal may impair soil macrofauna and related ecosystem services. To quantify straw removal effects on abundance, richness, and diversity of soil macrofauna, four experiments were conducted in São Paulo state, Brazil, under different edaphoclimatic conditions. A secondary goal was to evaluate seasonal changes on soil macrofauna and identify linkages between those changes and soil chemical and physical attributes. Four straw removal treatments (NR, no removal, LR, low removal, HR, high removal, and TR, total removal) were evaluated. Macrofauna and other soil attributes were sampled within the 0- to 0.30-m depth increment. Soil macrofauna were impaired by TR with the magnitude of response being related to both edaphoclimatic conditions and management practices. Numerous interactions among seasons, straw removal rates, and soil macrofauna were found, especially for total abundance and diversity of organisms. Partial straw removal (HR and LR) may be a strategy to protect soil health and increase bioenergy production with minimal effects on soil macrofauna, although long-term experiments are needed to confirm our hypothesis. The NR treatment generally had better soil quality as indicated by greater soil moisture, macropore number, soil organic carbon (SOC) content, and soil fertility, which led to a higher abundance of most macrofauna organisms. Total removal resulted in greater soil compaction and decreased macrofauna abundance, especially in clay soils. Our findings confirm that an integrated approach using soil indicators as guidelines should be adopted to better predict sustainable straw management practices for sugarcane in Brazil.

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.

This study evaluated the effect of different N fertilizer application methods on N2O and CH4 emissions and on sugarcane biomass yields over two successive growing seasons. Treatments included three methods of N fertilizer (120 kg ha(-1) N) application: 1) above the straw layer; 2) below the straw layer; 3) incorporated into the soil (at 0.1-m soil depth) below the straw layer; and 4) no N application (control). Sugarcane yield for the above straw treatment was, on average, 12% and 15% lower than below the straw and incorporated into the soil, respectively. Emissions of CH4 were very low and unaffected by N fertilizer placement. The method and timing of N application influenced N2O emissions. For both years, higher N2O emissions were observed from the above straw, followed by below straw and incorporated treatments. Except for the above straw treatment during the wet season, the N2O emission factors ranged from 0.08 to 0.62 and were lower than the IPCC default value (1%). The intensity of N2O emissions was, on average, 7.45, 3.97 and 3.3 kg CO(2)eq Mg stalk(-1) for N applied above straw, below straw and incorporated into the soil, respectively. Changes in the N fertilizer placement method and on the timing of application can significantly reduce GHG emissions during sugarcane production, making a significant contribution toward a cleaner production of sugarcane ethanol.

Industrial ethanol fermentation is subject to bacterial contamination that causes significant economic losses in ethanol fuel plants. Chronic contamination has been associated with biofilms that are normally more resistant to antimicrobials and cleaning efforts than planktonic cells. In this study, contaminant species of Lactobacillus isolated from biofilms (source of sessile cells) and wine (source of planktonic cells) from industrial and pilot-scale fermentations were compared regarding their ability to form biofilms and their sensitivity to different antimicrobials. Fifty lactobacilli were isolated and the most abundant species were Lactobacillus casei, Lactobacillus fermentum and Lactobacillus plantarum. The majority of the isolates (87.8%) were able to produce biofilms in pure culture. The capability to form biofilms and sensitivity to virginiamycin, monensin and beta-acids from hops, showed inter- and intra-specific variability. In the pilot-scale fermentation, Lactobacillus brevis, L. casei and the majority of L. plantarum isolates were less sensitive to beta-acids than their counterparts from wine; L. brevis isolates from biofilms were also less sensitive to monensin when compared to the wine isolates. Biofilm formation and sensitivity to beta-acids showed a positive and negative correlation for L. casei and L. plantarum, respectively.

Five different agricultural management systems and a forest fragment at two farms were investigated for effects on soil bacterial indicators. This study was conducted in southern Mato Grosso do Sul, Brazil, in January 2014, at two farms that incorporated integrated crop-livestock systems in Hapludox soil. Impacts of management were assessed through evaluation of functional bacterial communities using quantitative PCR (qPCR) of nitrogen cycling genes (amoA, nirK, and nosZ), PCR-DGGE of the nirK community composition, and by investigating relationships of the nirK community with soil properties. The nirK gene community showed that reference forest soil maintained relatively large nirK, nosZ, but small amoA gene abundances and large range weighted nirK richness (Rr). The introduction of pasture into crop-livestock integration management (inclusion of the second and third year of grazing within a crop-livestock integration system, CL-2 and CL-3, respectively) or the field in its first year of crop rotation after grazing pasture (CL-b) increased nosZ and amoA abundance. Three years of grazing pasture in crop-livestock integration (CL-a) increased nirK abundance, while multiple years of crop rotation in crop-livestock integration management systems increased soil OM and promoted a richer nirK community composition. The nirK community Rr that was not significantly different from the forest was observed in the second or third year of crop rotation after grazing (CL-c or CL-d, respectively) and (CL-3). In contrast, fields in pasture (CL-a, continuous pasture (CP)) and the first year of crop rotation after pasture (CL-b) had reduced Rr and functional organization curves, indicating communities less resilient to future stress. Management systems under integrated crop-livestock farming in tropical soil maintained a relatively diverse N cycling bacterial community, possibly promoting soil quality and N cycling processes.

Large-scale bioenergy demand has triggered new approaches to straw management in Brazilian sugarcane fields. With the progressive shift from a burned to a nonburned harvest system, most of the straw presently retained on the soil surface has become economically viable feedstock for bioenergy production. The trade-offs between the need to preserve soil quality and produce more bioenergy have been the subject of intense discussion. This study presents a synthesis of available information on the magnitude of the main impacts of straw removal from sugarcane fields for bioenergy production and therefore represents an easily available resource to guide management decisions on the recommended amount of straw to be maintained on the field to take advantage of the agronomic, environmental, and industrial benefits. Crop residues remaining on sugarcane fields provide numerous ecosystem services including nutrient recycling, soil biodiversity, water storage, carbon accumulation, control of soil erosion, and weed infestation. Furthermore, several studies reported higher sugarcane production under straw retention on the field, while few suggest that straw may jeopardize biomass production in cold regions and under some specific soil conditions. Pest control is among the parameters favored by straw removal, while N2O emissions are increased only if straw is associated with the application of N fertilizer and vinasse. An appropriate recommendation, which is clearly site specific, should be based on a minimum mass of straw on the field to provide those benefits. Overall, this review indicates that most of the agronomic and environmental benefits are achieved when at least 7 Mg ha(-1) of dry straw is maintained on the soil surface. However, modeling efforts are of paramount importance to assess the magnitude and rates of straw removal considering the several indicators involved in this complex equation, so that an accurate straw recovery rate could be provided to producers and industry toward greater sustainability.

We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.

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, N 2 O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes ( nos Z) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N 2 O. 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.

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.