Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia

Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir

Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.

Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs

Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.

Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir

Our comprehension of the dynamics and diversity of freshwater planktonic bacterial communities is far from complete concerning the Brazilian Amazonian region. Therefore, reference studies are urgently needed. We mapped bacterial communities present in the planktonic communities of a freshwater artificial reservoir located in the western Amazonian basin. Two samples were obtained from rainy and dry seasons, the periods during which water quality and plankton diversity undergo the most significant changes. Hypervariable 16S rRNA and shotgun sequencing were performed to describe the first reference of a microbial community in an Amazonian lentic system. Microbial composition consisted mainly of Betaproteobacteria, Cyanobacteria, Alphaproteobacteria, and Actinobacteria in the dry period. The bacteria distribution in the rainy period was notably absent of Cyanobacteria. Microcystis was observed in the dry period in which the gene cluster for cyanotoxins was found. Iron acquisition gene group was higher in the sample from the rainy season. This work mapped the first inventory of the planktonic microbial community of a large water reservoir in the Amazon, providing a reference for future functional studies and determining other communities and how they interact.

Archaea in Natural and Impacted Brazilian Environments

In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Seasonal effects in a lake sediment archaeal community of the Brazilian Savanna

The Cerrado is a biome that corresponds to 24% of Brazil's territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra's amoA gene. The principal coordinate analysis (PCoA) test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities.

Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress

Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH(4) production (analysis of CH(4) and δ(13) C of CH(4), CO(2) and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH(4), with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH(4) production even increased after desiccation-rewetting, demonstrating that the function of the methanogenic microbial community had not been impaired. This result indicates that the increase in extreme events of drying may increase methane production in flooded sediments.

Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area

Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order, which is known for its broad catabolic range among methanogens and is widespread throughout diverse environments. The draft genome of the strain presented here was cultivated from sediment samples collected from the Tucuruí hydroelectric power station reservoir.

Diversity of Archaea in Brazilian savanna soils

Although the richness of Bacteria and Fungi in Cerrado' soils has been reported, here we report, for the first time, the archaeal community in Cerrado's soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from 'cerrado denso' had greater Archaea richness than those from 'mata de galeria' based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.

Microbial and chemical characterization of underwater fresh water springs in the Dead Sea

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit.