Response of the bacterial communities associated with maize rhizosphere to poultry litter as an organomineral fertilizer.

Maize is an important food source worldwide and is of considerable industrial importance. Low maize yields are mostly due to low soil fertility, so expensive mineral fertilizers are often used to offset the lack of nutrients. Poultry litter (PL) is one of the most valuable and phosphorous-rich animal wastes. However, PL usually contains veterinary antibiotic residues, particularly fluoroquinolones (FQs), which may alter soil microorganism diversity and resistance patterns. In this study, we aimed to understand the impact of applying mineral (triple superphosphate?STP) or organomineral (STP with PL and reactive Bayovar phosphate with PL) fertilizers (130 or 260 kg/ha of total P2O5) on the structure and composition of the soil bacteriome and on phosphate-mineralizing bacteria associated with the maize rhizosphere. Maize plants were sampled at 60 and 90 days after sowing and a clear rhizosphere effect was observed in all samples. No specific groups of bacterial genera predominated (>3% relative abundance) according to the different fertilizer treatments and most of the genera were shared among samples. Multivariate analyses of 16S rRNA sequences revealed clear clustering based on sampling time and distinct separation from bulk soil samples. Abundances of phosphate-mineralizing bacteria varied depending on the sampling time.We observed a positive effect on phytase activity under the 260 kg STP with PL treatment. Although the FQ enrofloxacin and its main metabolite ciprofloxacin were detected in PL, their concentrations in fertilized soils were below quantification thresholds. Quinolone resistance genes were not detected in the maize rhizosphere or bulk soil. Together, these results suggest that the rhizosphere effect, plant age and applied amounts of fertilizer are more influential on bacterial communities than the type of fertilizer used. Thus, application of PL as an organomineral fertilizer does not appear to have extensive impacts on the bacterial diversity of maize rhizosphere, so it could be an excellent option for enhancing maize production

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem

Cultivation-Independent Methods Reveal Differences among Bacterial Gut Microbiota in Triatomine Vectors of Chagas Disease

Chagas disease is one of the most important endemic diseases of South and Central America. Its causative agent is the protozoan Trypanosoma cruzi, which is transmitted to humans by blood-feeding insects known as triatomine bugs. These vectors mainly belong to Rhodnius, Triatoma and Panstrongylus genera of Reduviidae. The bacterial communities in the guts of these vectors may have important effects on the biology of T. cruzi. For this reason, we analyzed the bacterial diversity hosted in the gut of different species of triatomines using cultivation-independent methods. Among Rhodnius sp., we observed similar bacterial communities from specimens obtained from insectaries or sylvatic conditions. Endosymbionts of the Arsenophonus genus were preferentially associated with insects of the Panstrongylus and Triatoma genera, whereas the bacterial genus Serratia and Candidatus Rohrkolberia were typical of Rhodnius and Dipetalogaster, respectively. The diversity of the microbiota tended to be the largest in the Triatoma genus, with species of both Arsenophonus and Serratia being detected in T. infestans

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Microbial Community Shift Under Exposure of Dredged Sediments From a Eutrophic Bay

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals—as indicators of complex contamination—dehydrogenase (DHA) and esterase enzymes (EST)—as indicators of microbial community availability—were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management

Microbial diversity and hydrocarbon depletion in low and high diesel-polluted soil samples from Keller Peninsula, South Shetland Islands

The bioremediation of Antarctic soils is a challenge due to the harsh conditions found in this environment. To characterize better the effect of total petroleum hydrocarbon (TPH) concentrations on bacterial, archaeal and microeukaryotic communities in low (LC) and high (HC) hydrocarbon- contaminated soil samples from the Maritime Antarctic clone libraries (small-subunit rRNA genes) were constructed. The results showed that a high concentration of hydrocarbons resulted in a decrease in bacterial and eukaryotic diversity; however, no effect of the TPH concentration was observed for the archaeal community. The HC soil samples demonstrated a high relative abundance of bacterial operational taxonomic units (OTUs) affiliated with unclassified group TM7 and eukaryotic OTUs affiliated with unclassified fungi from Pezizomycotina subphyla. Chemical analyses of the LC and HC soil samples revealed the presence of negligible amounts of nitrogen, thereby justifying the use of biostimulation to remediate these Antarctic soils. Microcosm experiments showed that the application of fertilizers led to an increase of up to 27.8% in the TPH degradation values. The data presented here constitute the first step towards developing the best method to deploy bioremediation in Antarctic soils and provide information to indicate an appropriate action plan for immediate use in the case of new accidents

Dissimilatory Iron-Reducing Microorganisms Are Present and Active in the Sediments of the Doce River and Tributaries Impacted by Iron Mine Tailings from the Collapsed Fundão Dam (Mariana, MG, Brazil)

On 5 November 2015, a large tailing deposit failed in Brazil, releasing an estimated 32.6 to 62 million m3 of iron mining tailings into the environment. Tailings from the Fundão Dam flowed down through the Gualaxo do Norte and Carmo riverbeds and floodplains and reached the Doce River. Since then, bottom sediments have become enriched in Fe(III) oxyhydroxides. Dissimilatory iron-reducing microorganisms (DIRMs) are anaerobes able to couple organic matter oxidation to Fe(III) reduction, producing CO2 and Fe(II), which can precipitate as magnetite (FeO·Fe2O3) and other Fe(II) minerals. In this work, we investigated the presence of DIRMs in affected and non-affected bottom sediments of the Gualaxo do Norte and Doce Rivers. The increase in Fe(II) concentrations in culture media over time indicated the presence of Fe(III)-reducing microorganisms in all sediments tested, which could reduce Fe(III) from both tailings and amorphous ferric oxyhydroxide. Half of our enrichment cultures converted amorphous Fe(III) oxyhydroxide into magnetite, which was characterized by X-ray diffraction, transmission electron microscopy, and magnetic measurements. The conversion of solid Fe(III) phases to soluble Fe(II) and/or magnetite is characteristic of DIRM cultures. The presence of DIRMs in the sediments of the Doce River and tributaries points to the possibility of reductive dissolution of goethite (α-FeOOH) and/or hematite (α-Fe2O3) from sediments, along with the consumption of organics, release of trace elements, and impairment of water quality