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This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR ( q-PCR) assays and pyrosequencing of 16 S r RNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16 S r RNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area. [ABSTRACT FROM AUTHOR]

The anoxic earthworm gut augments the activity of ingested microorganisms capable of anaerobiosis. Small earthworms ( Lumbricidae) emit denitrification-derived N2O, whereas the large Octochaetus multiporus ( Megascolecidae) does not. To examine this paradox, differently sized species of the families Glossoscolecidae ( Rhinodrilus, Glossoscolex, Pontoscolex), Megascolecidae ( Amynthas, Perionyx), Acanthodrilidae ( Dichogaster), and Eudrilidae ( Eudrilus) from Brazil were analyzed. Small species and the large Rhinodrilus alatus emitted N2O, whereas the large Glossoscolex paulistus did not, even though its gut could denitrify. N2 and N2O were emitted concomitantly, and R. alatus emitted the highest amount of N2. Denitrifiers and dissimilatory nitrate reducers were analyzed by barcoded amplicon pyrosequencing of narG, nirK, and nosZ. Gene sequences in gut and soil of the large G. paulistus were similar, whereas sequences in gut and soil of the small Amynthas gracilis were different and were also different compared with those of the gut and soil of G. paulistus. However, the denitrifying gut microbiota for both earthworms appeared to be soil-derived and dominated by Rhizobiales. The results demonstrated that (1) the emission of denitrification-derived N2O is widespread in different earthworm families, (2) large earthworms can also emit nitrogenous gases, and (3) ingested members of Rhizobiales are associated with this emission. [ABSTRACT FROM AUTHOR]

Xylella fastidiosa has a wide host range. Isolates of this bacterium that cause diseases in citrus (CVC) and grapes (PD) share 98% genome homology, and 95.7% amino acid identity. Drug resistance genes show a higher level of divergence and may be involved in the X. fastidiosa–host interaction. Antibiotic susceptibility of CVC and PD strains were compared utilizing the Etest strip method (AB Biodisk). Etest is applicable for fastidious slow-growing organisms due to its reproducibility. Results showed that the CVC strain was resistant to bacitracin, cefotaxime, and trimethoprim, and susceptible to chloramphenicol, erythromycin, gentamicin, kanamycin, streptomycin, and tetracycline. The PD strain was susceptible to all tested antibiotics, except kanamycin and trimethoprim. Both isolates produced a class C β-lactamase. These data support previous antibiotic studies and gene discrepancies found in the sequencing data of PD and CVC strains. These results demonstrate the efficacy of utilizing Etest assays for X. fastidiosa strains. [ABSTRACT FROM AUTHOR]

Understanding nanoparticle root uptake and root-to-shoot transport might contribute to the use of nanotechnology in plant nutrition. This study performed time resolved experiments to probe Zn uptake, biotransformation and physiological effects on Phaseolus vulgaris (L.). Plants roots were exposed to ZnO nanoparticles (40 and 300 nm) dispersions and ZnSO4(aq) (100 and 1000 mg Zn L−1) for 48 h. Near edge X-ray absorption spectroscopy showed that 40 nm ZnO was more easily dissolved by roots than 300 nm ZnO. It also showed that in the leaves Zn was found as a mixture Zn3(PO4)2 and Zn-histidine complex. X-ray fluorescence spectroscopy showed that root-to-shoot Zn-translocation presented a decreasing gradient of concentration and velocity, it seems radial Zn movement occurs simultaneously to the axial xylem transport. Below 100 mg Zn L−1, the lower stem tissue section served as a buffer preventing Zn from reaching the leaves. Conversely, it was not observed for 1000 mg Zn L−1 ZnSO4(aq). Transcriptional analysis of genes encoding metal carriers indicated higher expression levels of tonoplast-localized transporters, suggesting that the mechanism trend to accumulate Zn in the lower tissues may be associated with an enhanced of Zn compartmentalization in vacuoles. The photosynthetic rate, transpiration, and water conductance were impaired by treatments. [ABSTRACT FROM AUTHOR]

Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.