Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance

Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities

Diversidade e potencial biotecnológico da comunidade bacteriana endofítica de sementes de soja

The objectives of this work were to isolate, characterize and identify the endophytic bacterial community of soybean seeds, and to test the biotechnological potential of this community. Seeds from 12 soybean cultivars were used. The endophytic bacterial isolates were evaluated for in vitro antagonism against phytopathogenic fungi, synthesis of indoleacetic acid (IAA), and capacity to solubilize phosphate. Isolation techniques, (ARDRA) grouping, and identification by means of partially sequencing the 16S rDNA were used in community characterization. The isolates with best biotechnological potential were inoculated in seeds to evaluate their ability to promote plant growth. Twelve ribotypes were identify by means of ARDRA and classified as: Acinetobacter, Bacillus, Brevibacterium, Chryseobacterium, Citrobacter, Curtobacterium, Enterobacter, Methylobacterium, Microbacterium, Micromonospora, Pantoea, Paenibacillus, Pseudomonas, Ochrobactrum, Streptomyces and Tsukamurella. As for the biotechnological potential of the community, 18% of the isolates were able to antagonize phytopathogenic fungi, 100% to synthesize IAA, and 39% to solubilize phosphate. The strain 67A(57) of Enterobacter sp. increased significantly the dry root biomass. Inoculation of promising isolates did not promote growth in soybean plants in most of the cases.O objetivo deste trabalho foi isolar, caracterizar e identificar a comunidade bacteriana endofítica de sementes de soja e avaliar o seu potencial biotecnológico. Foram utilizadas sementes de 12 cultivares de soja. Os isolados bacterianos endofíticos obtidos foram avaliados in vitro quanto ao antagonismo a fungos fitopatogênicos, síntese de ácido indolacético (AIA) e solubilização de fosfato. A caracterização foi realizada com técnicas de isolamento, análise de restrição do DNA ribossomal amplificado (ARDRA) e sequenciamento parcial do gene 16S rDNA. Os isolados com maior potencial biotecnológico foram inoculados em sementes de soja, para se avaliar a capacidade de promoção de crescimento de plantas. Foi possível identificar 12 ribótipos por meio da ARDRA, que foram classificados como: Acinetobacter, Bacillus, Brevibacterium, Chryseobacterium, Citrobacter, Curtobacterium, Enterobacter, Methylobacterium, Microbacterium, Micromonospora, Pantoea, Paenibacillus, Pseudomonas, Ochrobactrum, Streptomyces e Tsukamurella. Quanto ao potencial biotecnológico da comunidade, 18% dos isolados controlaram o crescimento de fungos fitopatogênicos, 100% produziram AIA, e 39% solubilizaram fosfato. O isolado 67A(57) de Enterobacter sp. aumentou significativamente a massa de matéria seca da raiz. A inoculação de isolados com elevado potencial biotecnológico em avaliações in vitro não promoveu o crescimento de plantas de soja na maioria dos casos

Linking the composition of bacterial and archaeal communities to characteristics of soil and flora composition in the Atlantic rainforest

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning

Screening of endoglucanase-producing bacteria in the saline rhizosphere of Rhizophora mangle

In screening the culturable endoglucanase-producing bacteria in the rhizosphere of Rhizophora mangle, we found a prevalence of genera Bacillus and Paenibacillus. These bacteria revealed different activities in endoglucolysis and biofilm formation when exposed to specific NaCl concentrations, indicating modulated growth under natural variations in mangrove salinity

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10³ in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments

Diversity of archaea and bacteria involved in the nitrogen cycling in mangrove sediments

O manguezal é um ecossistema costeiro, localizado em regiões de interface entre os ambientes terrestre e marinho, de ocorrência exclusiva em zonas tropicais e subtropicais. Esta localização confere ao sedimento deste ambiente características únicas, como alta salinidade e baixa disponibilidade de oxigênio, associado a grande riqueza em matéria orgânica. O resultado destas condições é a ocorrência de uma restrita diversidade de plantas em tais ambientes, associada a uma grande diversidade de animais, que usam o manguezal para sua proteção e reprodução. O presente estudo mostrou como as comunidades de arquéias (amoA e 16S DNAr) e bactérias (nifH e 16S DNAr) estão estruturadas em sedimentos de manguezais sob distintos estados de preservação. Os perfis de DGGE indicaram alterações na composição das comunidades alvo, ligando sua estruturação com a contaminação do ambiente, enquanto que as quantificações de tais genes por meio de PCR quantitativo em tempo real (qPCR) indicaram alterações apenas na comunidade de arquéias oxidadoras de amônio. A filogenia destes grupos revelou a presença de grupos comumente encontrados em solos e água, alem de grupos particulares, possivelmente relacionado ao processo de especiação no ambiente de manguezal. De maneira geral, os resultados indicam que as comunidades de arquéias e bactérias são responsivas ao estado de contaminação dos manguezais, o que pode gerar um processamento diferencial do nitrogênio nestes sedimentosThe mangrove is a coastal ecosystem, located in the interface regions between the land and sea environments, with exclusive occurrence in tropical and subtropical areas. Such location confers to the mangrove sediments unique characteristics, like as high salinity and low availability of oxygen, associated with the high abundance of organic matter. The result of these conditions is the occurrence of a restrict plant diversity, associated with a great diversity of animals, who use the mangroves for its protection and reproduction. The present study has shown how the communities of archaea (16S DNAr and amoA) and bacteria (16S DNAr and nifH) are structured in mangrove soils under distinct states of preservation. The DGGE patterns indicate alterations in the composition of targeted communities, linking its structure with the environmental contamination, while the quantifications of targeted genes by real time PCR (qPCR) has indicated alterations only in the community of ammonium oxidizers archaea. The phylogeny of these groups revealed the presence of groups commonly found in soils and water samples, besides the occurrence of particular groups, possibly resulted from a speciation process in the mangrove environment. In general, results indicated that archaeal and bacterial communities are responsive to the mangroves contamination, and its alteration can also lead to differential nitrogen processing in these soil

Bacterial diversity in sediment from mangrove of the island Cardoso Cananéia - São Paulo.

O presente trabalho busca entender a dinâmica de comunidades bacterianas cultiváveis e não cultiváveis do ecossistema do manguezal e prospectar nesse ambiente ainda inexplorado, um possível potencial biotecnológico. As amostras de sedimentos foram retiradas de duas profundidades no inverno e no verão. Bactérias caracterizadas por meio da técnica de ARDRA pertencem as ordens Vibrionales, Bacillales e Actinomycetales. As espécies bacterianas cultiváveis e as não cultiváveis foram também avaliadas por meio da técnica de PCR-DGGE, onde utilizou-se iniciadores seletivos para Actinobacterias, a e b Proteobacteria, Pseudomonas spp. e Paenibacillus spp., além do universal para bacteria. A análise multivariada de redundância (RDA) permitiu verificar a relação dos perfis obtidos das amostras com os fatores ambientais. Verificou-se uma diferente distribuição dos grupos de a e b Proteobacteria em relação à sazonalidade, enquanto que a profundidade de amostragem mostrou ser essencial no perfil das comunidades totais, a e b-Proteobacteria e Actinobacterias.The objective of the present work is the understanding of culturable and non-culturable bacterial community dynamic present in the mangrove ecosystem also to explore the biotechnological potential of bacteria present in this environmental. Sediment samples were obtained from two depths winter and summer seasons and further analyzed. The Bacteria were characterized by ARDRA and identified the orders Vibrionales, Bacillales e Actinomycetales. Culturable and non-culturable bacteria were also assessed by PCR-DGGE using specific primers for Actinobacteria, a-Proteobacteria, b-proteobacteria, Pseudomonas spp., Paenibacillus spp. and bacteria universal primers. Multivariate redundancy analysis allowed the verification of main factors determining the bacterial communities patterns found on samples. It was verified a seasonal distribution of a and b-Proteobacteria groups, while the sampled depth was determinant for the total bacterial community composition, and also influenced the a and b-Proteobacteria and Actinobacteria profiles

The parA region of broad-host-range PromA plasmids is a carrier of mobile genes

The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms