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1.
Environ Res ; 212(Pt A): 113139, 2022 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-35337832

RESUMO

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.

2.
ISME J ; 16(3): 726-737, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-34580430

RESUMO

The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.


Assuntos
Microbiota , Solo , Biodiversidade , Solo/química , Microbiologia do Solo
3.
Mol Ecol ; 30(11): 2560-2572, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33817881

RESUMO

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.


Assuntos
Euryarchaeota , Metano , Archaea/genética , Brasil , RNA Ribossômico 16S/genética , Microbiologia do Solo
4.
Sci Rep ; 9(1): 17101, 2019 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-31745137

RESUMO

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.


Assuntos
Proteínas Arqueais/metabolismo , Methanosarcina/crescimento & desenvolvimento , Methanosarcina/metabolismo , Fosfotransferases (Aceptor do Grupo Fosfato)/metabolismo , Polifosfatos/metabolismo , Anaerobiose , Proteínas Arqueais/genética
5.
J Environ Manage ; 196: 476-486, 2017 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-28343049

RESUMO

Over three million tonnes of spent mushroom substrate (SMS) are produced in Europe every year as a by-product of the cultivation of Agaricus bisporus. The management of SMS has become an increasing challenge for the mushroom production industry, and finding environmentally and economically sustainable solutions for this organic residue is, therefore, highly desirable. Due to its physical properties and nutrient content, SMS has great potential to be employed in agricultural and horticultural sectors, and further contribute to reduce the use of non-renewable resources, such as peat. However, SMS is often regarded as not being stable and/or mature, which hampers its wide use for crop production. Here, we demonstrate the stabilisation of SMS and its subsequent use as organic fertiliser and partial peat replacement in horticulture. The stabilisation was performed in a laboratory-scale composting system, with controlled temperature and aeration. Physical and chemical parameters were monitored during composting and provided information on the progress of the process. Water soluble carbohydrates (WSC) content was found to be the most reliable parameter to predict SMS stability. In situ oxygen consumption indicated the main composting phases, reflecting major changes in microbial activity. The structure of the bacterial community was also found to be a potential predictor of stability, as the compositional changes followed the composting progress. By contrast, the fungal community did not present clear successional process along the experiment. Maturity and quality of the stabilised SMS were assessed in a horticultural growing trial. When used as the sole fertiliser source, SMS was able to support Lolium multiflorum (Italian ryegrass) growth and significantly improved grass yield with a concentration-dependent response, increasing grass biomass up to 300%, when compared to the untreated control. In summary, the results indicated that the method employed was efficient in generating a stable and mature product, which has a great potential to be applied in horticulture. This study represents a step forward in the management of SMS residue, and also provides an alternative to reduce the use of peat in horticulture, alleviating environmental impacts to peatland ecosystems.


Assuntos
Agaricales , Agricultura , Fertilizantes , Europa (Continente) , Solo
6.
Front Microbiol ; 6: 779, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26284056

RESUMO

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.

7.
Mol Ecol ; 23(12): 2988-99, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24806276

RESUMO

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.


Assuntos
Ecossistema , Microbiologia do Solo , Agricultura , Ciclo do Carbono , Genes Bacterianos , Genes Fúngicos , Variação Genética , Metagenoma , Família Multigênica , Ciclo do Nitrogênio , Análise de Sequência com Séries de Oligonucleotídeos , Árvores , Clima Tropical
8.
ISME J ; 8(7): 1548-50, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24451208

RESUMO

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.


Assuntos
Conservação dos Recursos Naturais , DNA Fúngico/genética , DNA Ribossômico/genética , Fungos/genética , Raízes de Plantas/microbiologia , Microbiologia do Solo , Brasil , Código de Barras de DNA Taxonômico , Ecossistema , Fungos/classificação , Filogenia , Raízes de Plantas/classificação , Raízes de Plantas/genética , Árvores/classificação , Árvores/genética , Árvores/microbiologia , Clima Tropical
9.
Proc Natl Acad Sci U S A ; 110(3): 988-93, 2013 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-23271810

RESUMO

The Amazon rainforest is the Earth's largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.


Assuntos
Agricultura , Bactérias/isolamento & purificação , Biodiversidade , Microbiologia do Solo , Clima Tropical , Animais , Bactérias/classificação , Bactérias/genética , Brasil , Bovinos , Ecossistema , Humanos , Filogenia , Chuva , Árvores
10.
Food Chem Toxicol ; 47(1): 163-70, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19022329

RESUMO

The tamarind (Tamarindus indica L.) is indigenous to Asian countries and widely cultivated in the American continents. The tamarind fruit pulp extract (ExT), traditionally used in spices, food components and juices, is rich in polyphenols that have demonstrated anti-atherosclerotic, antioxidant and immunomodulatory activities. This study evaluated the modulator effect of a crude hydroalcoholic ExT on some peripheral human neutrophil functions. The neutrophil reactive oxygen species generation, triggered by opsonized zymosan (OZ), n-formyl-methionyl-leucyl-phenylalanine (fMLP) or phorbol myristate acetate (PMA), and assessed by luminol- and lucigenin-enhanced chemiluminescence (LumCL and LucCL, respectively), was inhibited by ExT in a concentration-dependent manner. ExT was a more effective inhibitor of the PMA-stimulated neutrophil function [IC50 (in microg/10(6)cells)=115.7+/-9.7 (LumCL) and 174.5+/-25.9 (LucCL)], than the OZ- [IC50=248.5+/-23.1 (LumCL) and 324.1+/-34.6 (LucCL)] or fMLP-stimulated cells [IC50=178.5+/-12.2 (LumCL)]. The ExT also inhibited neutrophil NADPH oxidase activity (evaluated by O2 consumption), degranulation and elastase activity (evaluated by spectrophotometric methods) at concentrations higher than 200 microg/10(6)cells, without being toxic to the cells, under the conditions assessed. Together, these results indicate the potential of ExT as a source of compounds that can modulate the neutrophil-mediated inflammatory diseases.


Assuntos
Frutas/química , Neutrófilos/efeitos dos fármacos , Neutrófilos/metabolismo , Extratos Vegetais/farmacologia , Tamarindus/química , Antioxidantes/química , Antioxidantes/farmacologia , Degranulação Celular/efeitos dos fármacos , Células Cultivadas , Feminino , Humanos , Medições Luminescentes , Masculino , NADPH Oxidases/antagonistas & inibidores , Elastase Pancreática/antagonistas & inibidores , Ésteres de Forbol , Extratos Vegetais/química , Espécies Reativas de Oxigênio/metabolismo
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