Rhizobacteria control damping-off and promote growth of lima bean with and without co-inoculation with Rhizobium tropici CIAT899.

Rhizoctonia solani compromises the production of lima bean, an alternative and low-input food source in many tropical regions. Inoculation of bacterial strains has been used, but research on their biocontrol and growth promotion potential on lima bean is scarce. The objective of this study was to evaluate the effects of inoculation with rhizobacterial strains of the genera Bacillus, Brevibacillus, Paenibacillus, Burkholderia, Pseudomonas, and Rhizobium in combination or not with N2-fixing Rhizobium tropici on the control of damping-off disease and growth promotion in lima bean plants. Greenhouse experiments were conducted to evaluate the inoculation with bacterial strains with biocontrol potential in combination or not with R. tropici in substrate infected with R. solani CML 1846. Growth promotion of these strains was also assessed. Strains of Brevibacillus (UFLA 02-286), Pseudomonas (UFLA 02-281 and UFLA 04-885), Rhizobium (UFLA 04-195), and Burkholderia (UFLA 04-227) co-inoculated with the strain CIAT 899 (Rhizobium tropici) were the most effective in controlling R. solani, reducing the disease incidence in 47-60% on lima bean. The promising strains used in the biocontrol assays were also responsive in promoting growth of lima bean under disease and sterile conditions. A positive synergistic effect of co-inoculation of different genera contributed to plant growth, and these outcomes are important first steps to improve lima bean production.

Polymeric formulations of liquid inoculants with rhizobia exopolysaccharides increase the survival and symbiotic efficiency of elite Bradyrhizobium strains.

We studied the survival of four elite strains of Bradyrhizobium in liquid inoculants with three formulations with exopolysaccharides extracted from other rhizobia genera, and the symbiotic efficiency of these elite strains with soybean and cowpea in a greenhouse. For that purpose, we verified the effectiveness of formulations for maintaining the cell viability of strains by counting the colony-forming units (CFU) per milliliter of the liquid inoculants with formulations after 90 days. For survival of the soybean inoculant strains, 29W and CPAC15, the largest number of CFU (> 1010 mL-1) after 90 days was observed in the PEPS formulation. For the cowpea inoculant strains, INPA3-11B and UFLA3-84, the REPS1 formulation had the largest number of CFU (> 1010 mL-1) after 90 days. The symbiotic efficiency of the PEPS formulation, followed by REPS2, was higher than that shown by the commercial inoculant in soybean. For cowpea, the three formulations with EPS, especially REPS1, showed symbiotic efficiency better than that of the commercial inoculant.

Ecological co-occurrence and soil physicochemical factors drive the archaeal community in Amazonian soils.

We evaluated the co-occurrence of archaeal taxonomic groups and soil physicochemical characteristics in relation to the structuring of the archaeal community in Amazonian soil under different land use systems. Soil samples were collected in primary forest (PF), secondary forest (SF), agricultural systems (AG) and cattle pastures (PA). Archaeal community composition was revealed based on high-throughput amplicon sequencing of the 16S rRNA gene. The results revealed co-occurrence of archaeal classes, with two groups formed: Thaumarchaeota classes, including South Africa Gold Mine-Group 1 (SAGMG-1), Crenarchaeotic group (SCG) and Crenarchaeota candidate division YNPFFA, with predominance in PF and SF; and Bathyarchaeota_unclassified, Methanomicrobia and Methanobacteria (Euryarchaeota) with the FHMa11 terrestrial group, with predominance in PA. The number of co-occurrences between groups was lower in SF, AG and PA (approximately 30%) than in PF. The qPCR analysis revealed that PF also had the largest number of archaeal representatives. Soil texture may be a limiting factor of interactions between groups since the most representative groups, SAGMG-1 and the SCG (over 20% in all sites), were positively associated with coarse sand, the soil factor most correlated with the groups (33% of the total). These results suggest that interactions between archaeal classes belonging to different phyla may be dependent on the number of individuals in the soil environment. In this context, differences in soil physical structure among the land use systems can reduce the representatives of key groups and consequently the co-occurrence of Archaea, which could compromise the natural dynamics of this complex environment.

Diversity and Efficiency of Rhizobia from a Revegetated Area and Hotspot-Phytophysiognomies Affected by Iron Mining as Indicators of Rehabilitation and Biotechnological Potential.

This study aimed to evaluate the resilience of phytophysiognomies under influence of iron mining by assessing the occurrence, diversity, and symbiotic efficiency of native communities of nitrogen-fixing bacteria that nodulate leguminous plants (rhizobia) in soils of an area revegetated with grass after iron mining activities and in the phytophysiognomies in adjacent areas (Canga, Atlantic Forest, Cerrado, and Eucalyptus-planted forest). Experiments for capturing rhizobia through two species of promiscuous plants, siratro (Macroptilium atropurpureum) and cowpea (Vigna unguiculata), were conducted in a greenhouse. The rhizobial strains isolated were characterized phenotypically, genetically (16S rRNA sequencing and BOX-PCR fingerprinting), and regard symbiotic efficiency of biological nitrogen fixation (BNF) compared to mineral nitrogen and reference strains. Cowpea captured a higher density of rhizobia than siratro did. However, most of the strains captured by siratro had greater symbiotic efficiency. The revegetated area proved to be the community most efficient in N2 fixation and was also the most diverse, whereas Canga was the least diverse. For the two trap species, the predominant genus captured in the revegetated area and in the phytophysiognomies was Bradyrhizobium. The greater symbiotic efficiency and the high genetic diversity of the rhizobial community in the revegetated area indicate the effectiveness of the soil rehabilitation process. The revegetated area and the phytophysiognomies proved to harbor strains with high biotechnological potential. Results indicate that the high functional redundancy of this group of bacteria contributes to the resilience of these phytophysiognomies and the revegetated area.

Bradyrhizobium campsiandrae sp. nov., a nitrogen-fixing bacterial strain isolated from a native leguminous tree from the Amazon adapted to flooded conditions.

The nitrogen-fixing bacterial strain UFLA 01-1174T was isolated from nodules of Campsiandra laurilifolia Benth. originating from the Amazon region, Brazil. Its taxonomic position was defined using a polyphasic approach. Analysis of the 16S rRNA gene placed the strain in the Bradyrhizobium genus, the closest species being B. guangdongense CCBAU 51649T and B. guangzhouense CCBAU 51670T, both with 99.8% similarity. Multilocus sequence analysis (MLSA) of recA, gyrB, glnII, rpoB, atpD, and dnaK indicated that UFLA 01-1174T is a new species, most closely related to B. stylosanthis BR 446T (94.4%) and B. manausense BR 3351T (93.7%). Average nucleotide identity (ANI) differentiated UFLA 01-1174T from the closest species with values lower than 90%. The G + C content in the DNA of UFLA 01-1174T is 63.6 mol%. Based on this data, we conclude that the strain represents a new species. The name proposed is Bradyrhizobium campsiandrae, with UFLA 01-1174T (= INPA 394BT = LMG 10099T) as type strain.

Chemical, physical, and biological attributes in soils affected by deposition of iron ore tailings from the Fundão Dam failure.

Monitoring degraded areas is essential for evaluation of the quality of the rehabilitation process. In this study, we evaluate how the physical and chemical characteristics of the mixture of iron ore tailings with the soil have affected the soil microbial biomass and activity in areas along the Gualaxo do Norte River after the Fundão Dam disaster. Composite soil samples were collected from areas that were impacted (I) and not impacted (NI) by the tailings. The following attributes were evaluated: chemical element content; soil density, porosity, and texture; microbial biomass carbon; basal respiration; and enzyme activity and density of microbial groups (bacteria, actinobacteria, fungi, arbuscular mycorrhizae, phosphate solubilizers, cellulolytic microorganisms, nitrifiers, ammonifiers, and diazotrophs). According to result, the deposition of tailings increased the pH and the soil available P, Cr, Fe, and Mn content and reduced organic matter. The physical and biological attributes were negatively affected, with increases in the silt content and density of the soil, and reduction in macroporosity and in the microbial biomass and activity of the soil (respiration and enzymes) in the impacted area. However, the impacted areas exhibited greater densities of some microbial groups (cellulolytic microorganisms, nitrifiers, and diazotrophic bacteria). Modifications in the organic matter and silt content are the main attributes associated with deposition of the tailings that affected soil microbial biomass and microbial activity. This may affect erosive conditions and the functionality of the ecosystem, indicating an imbalance in this environment. In contrast, the higher density of some microbial groups in the impacted areas show the high rehabilitation potential of these areas.

Bradyrhizobium uaiense sp. nov., a new highly efficient cowpea symbiont.

This study describes two Bradyrhizobium strains, UFLA03-164T and UFLA03-153, which share more than 99% sequence similarity of the 16S rRNA with the type strains of 15 species in this genus. The concatenation of three housekeeping genes (recA, gyrB, and dnaK) indicated that both strains formed a single clade separate from known Bradyrhizobium species. B. viridifuturi, represented by SEMIA 690T, is the closest neighboring species (96.2%). Low (< 92%) average nucleotide identity (ANI) was observed between strain UFLA03-164T and any of the closest species on the phylogenetic trees based on concatenated housekeeping genes. The DNA G+C content of UFLA03-164T is 63.25%. Phenotypic characteristics were determined for both UFLA strains. Based on the data, the two strains represent a new species for which the name Bradyrhizobium uaiense is proposed, with UFLA03-164T (= LMG 31509T) as type strain.

Efficient Nitrogen-Fixing Bacteria Isolated from Soybean Nodules in the Semi-arid Region of Northeast Brazil are Classified as Bradyrhizobium brasilense (Symbiovar Sojae).

Soybean (Glycine max L.) is an important legume that greatly benefits from inoculation with nitrogen-fixing bacteria. In a previous study, five efficient nitrogen-fixing bacterial strains, isolated from nodules of soybean inoculated with soil from semi-arid region, Northeast Brazil, were identified as a new group within the genus Bradyrhizobium. The taxonomic status of these strains was evaluated in this study. The phylogenetic analysis of the 16S rRNA gene showed the high similarity of the five strains to Bradyrhizobium brasilense UFLA03-321T (100%), B. pachyrhizi PAC48T (100%), B. ripae WR4T (100%), B. elkanii USDA 76T (99.91%), and B. macuxiense BR 10303T (99.91%). However, multilocus sequence analysis of the housekeeping genes atpD, dnaK, gyrB, recA, and rpoB, average nucleotide identity, and digital DNA-DNA hybridization analyses supported the classification of the group as B. brasilense. Some phenotypic characteristics allowed differentiating the five strains and the type strain of B. brasilense from the two neighboring species (B. pachyrhizi PAC48T and B. elkanii USDA 76T). The nodC and nifH genes' analyses showed that these strains belong to symbiovar sojae, together with B. elkanii (USDA 76T) and B. ferriligni (CCBAU 51502T). The present results support the classification of these five strains as Bradyrhizobium brasilense (symbiovar sojae).

Trends in Brazilian Congress of Soil Science publications: An analysis of the 1947-2017 period.

The Brazilian Congress of Soil Science (Congresso Brasileiro de Ciência do Solo - CBCS) is the oldest soil science event in South America. The CBCS had 29,643 participants and 23,621 publications in 30 thematic areas between 1947 and 2017. There were only five editions of the CBCS (1947-1979) in which Soil Fertility did not produce the highest number of papers. Standardization of Soil Study Methods and Representation/Soil Teaching was the most prolific in one year, and Soil Genesis, Morphology, and Cartography produced the most papers in the other four years. Subsequently, the area renamed as Soil Fertility and Plant Nutrition had the highest number of papers. By grouping papers into the scientific divisions of the Brazilian Society of Soil Science (Sociedade Brasileira de Ciência do Solo - SBCS), we verify that the division of Soil Use and Management had the most papers in most congresses. In 2017, the number of papers and the number of male researchers in the Brazilian National Council for Scientific and Technological Development were associated for each thematic area. The trends in CBCS publications were influenced by the natural and historic-economic characteristics of the country, in addition to changes that occurred in SBCS, universities, research institutes, and legislation.

Formononetin accelerates mycorrhization and increases maize production at low phosphorus application rates.

The formononetin biostimulant may be an option for reducing P fertilization once it stimulates mycelial growth of arbuscular mycorrhizal fungi and increases plant ability to take up nutrients through the roots, especially phosphorus. The objective of this study was to evaluate the effect of formononetin associated with phosphorus fertilization in maize. Field experiments were conducted in a randomized block design with a 3 × 4 factorial arrangement (0, 50 or 70, and 140 kg ha-1 P2O5; and formononetin application rates: 0, 25, 50, and 100 g ha-1), with four replications. Formononetin (100 g ha-1) increased the mycorrhizal colonization rate up to 30% in maize in the first four weeks after emergence when no P fertilizer was applied, and to 17% when 50 or 70 kg ha-1 of P2O5 were applied. The application of 50 and 100 g ha-1 of formononetin significantly increased plant height, ear height, and grain yield (22% - 76%) when no P fertilizer was applied. The use of formononetin in the field stimulates mycorrhizal colonization, has a positive effect on maize yield, and reduces the need for P fertilizer application in maize. However, this effect was evident only at low P soil contents.

Microbiological Indicators of Soil Quality Under Native Forests are Influenced by Topographic Factors.

Several microbiological indicators of soil quality present high sensitivity, but little is known about the influence of topographic factors on them. This work aimed to evaluate variability of biological indicators of soil quality across a hillslope under native forest and the influence of topographic factors on them. Four positions on a hillslope were evaluated. Activity of the enzymes ß-glucosidase, acid phosphatase, urease and fluorescein diacetate (FDA) hydrolysis were determined, as well as basal and substrate-induced respiration, and density of microorganisms: total bacteria, total fungi, actinobacteria, phosphate solubilizers, ammonifiers, native rhizobia, free-living N2-fixing bacteria, spores of arbuscular mycorrhizal fungi and percentage of root colonization by arbuscular mycorrhizal fungi. Activity and density of microorganisms were correlated with topographic factors. The relation of these factors to the variations of the evaluated indicators was determined using the random forest algorithm. Microbiological indicators varied according to the hillslope positions. The indicators urease, basal respiration, spore density, mycorrhizal colonization, total bacteria and fungi, phosphate solubilizers, and free-living N2-fixing bacteria detected in JNFB and FAM culture medium did not vary with terrain attributes and were therefore more indicated in cases of topographic variations. This and future studies can help to select the best microbiological indicators for different conditions.

Mn concentration and mycorrhizal colonization in understory native species grown at areas of manganese mine tailings disposal.

Revegetation of areas with mine tailings should consider not only the best technique but also the choice of species adapted to this condition. This study aimed to analyze the occurrence of plant species, their Mn concentrations, and mycorrhizal colonization after implementation of two revegetation techniques (replacement of topsoil with natural seed bank and planting of seedlings) in an area of disposal of tailings from Mn processing compared to a native forest area as well as to a place that was not revegetated. Plant samples (at least three individuals/species) were collected from the understory at revegetated locations and forest. The established plant species and their Mn concentrations, mycorrhizal colonization, and forms of Mn in the soil were analyzed. The use of topsoil led to greater plant diversity. The high concentrations of Mn in the substrates did not affect the occurrence of vegetation in the understory and mycorrhizal colonization. The plant species established in the revegetated areas differed in relation to Mn concentration (471-27,842 mg kg-1 in leaves), Mn translocation factor (0.2-125.3) and mycorrhizal colonization rates (1-35%). Four potential Mn hyperaccumulators species were identified: Aparisthmium cordatum, Clidemia hirta, Socratea exorrhiza, and Vismia latifolia.

Ionic speciation and risks associated with agricultural use of industrial biosolid applied in Inceptisol.

The evaluation of the chemical leaching potential from soils amended with biosolid is of extreme importance for environmental safety of agricultural use of these residues. The objective of this study was to evaluate the polluting potential and possible risks associated with the agricultural use of biosolids generated by the polyethylene terephthalate (PET) fiber and resin industry through ionic speciation and analysis of the activity of chemical species present in the leached solution from Inceptisol treated with rates 0, 6, 12, 18, 24, 48, 96, and 144 Mg ha-1 on dry basis. The experiment was conducted in a lysimeter and the treatments with three replications were distributed at random. Chemical leaching was made by application of CaC12 0.01 mol L-1 solutions in a volume fourfold higher than the water retention capacity of the soil, divided into five leaching events: 210, 245, 280, 315, and 350 days of incubation. Chemical species concentrations in collected leachates were used for ionic speciation by geochemical software Visual MINTEQA2 version 4.0. Impact factor of chemical species was calculated as the ratio between maximum concentration in the leach solution in the treated soil and control. Dissolved organic carbon had strong influence on Pb+2 and Cu+2 leaching, but these elements in free or complexed forms presented low activities in solution. Leaching of NO3-, Zn+2, and Na+ represents the main environmental risk of agricultural use of this residue. However, these risks can be minimized if technical criteria and critical limits for the agronomic use of biosolids were observed.

Bradyrhizobium forestalis sp. nov., an efficient nitrogen-fixing bacterium isolated from nodules of forest legume species in the Amazon.

Three strains of nitrogen-fixing bacteria isolated from nodules of Inga sp. (INPA54BT) and Swartzia sp. (INPA86A and INPA01-91A) in soils under native forest in the Brazilian Amazon were previously identified as belonging to the Bradyrhizobium genus. In this study, these strains were characterized using a polyphasic approach to establish their taxonomic position. The three strains shared more than 99.5% sequence similarity of the 16S rRNA gene with the type strains of five Bradyrhizobium species (B. japonicum USDA 6T, B. liaoningense LMG 18230T, B. ottawaense OO99T, B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T). However, multilocus sequence analysis of two (recA and glnII) or three (atpD, gyrB, and recA) housekeeping genes indicated that these three strains represent a new Bradyrhizobium species, which is closely related to B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. DNA-DNA hybridization values between INPA54BT and B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T were only 41.5 and 30.9%, respectively. Phenotypic characterization also allowed the differentiation of the novel species from B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. In the phylogenetic analysis of the nodC and nifH genes, the three strains showed similar sequences that were divergent from those of type strains of all Bradyrhizobium species. We concluded that these strains represent a novel species, for which the name Bradyrhizobium forestalis is proposed, with INPA54BT (= LMG 10044T) as type strain. The G+C content in the DNA of INPA54BT is 63.7 mol%.

Assessment of the occurrence and richness of arbuscular mycorrhizal fungal spores by direct analysis of field samples and trap culture - a comparative study.

In this work, we hypothesized that two spore-based methods, direct analysis of field samples and trap cultures, simultaneously used for assessment of occurrence and species richness of arbuscular mycorrhizal fungi (AMF) may vary in their efficiency according to the environmental conditions and the total AMF species richness of the evaluated ecosystem. The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. Analysis of dataset 2 showed that the relative performance of trap cultures, using direct analysis of field sample as reference, was inversely related to the total observed AMF species richness.

Effectiveness of Arbuscular Mycorrhizal Fungal Isolates from the Land Uses of Amazon Region in Symbiosis with Cowpea.

Arbuscular mycorrhizal fungi provide several ecosystem services, including increase in plant growth and nutrition. The occurrence, richness, and structure of arbuscular mycorrhizal fungi communities are influenced by human activities, which may affect the functional benefits of these components of the soil biota. In this study, 13 arbuscular mycorrhizal fungi isolates originating from soils with different land uses in the Alto Solimões-Amazon region were evaluated regarding their effect on growth, nutrition, and cowpea yield in controlled conditions using two soils. Comparisons with reference isolates and a mixture of isolates were also performed. Fungal isolates exhibited a wide variability associated with colonization, sporulation, production of aboveground biomass, nitrogen and phosphorus uptake, and grain yield, indicating high functional diversity within and among fungal species. A generalized effect of isolates in promoting phosphorus uptake, increase in biomass, and cowpea yield was observed in both soils. The isolates of Glomus were the most efficient and are promising isolates for practical inoculation programs. No relationship was found between the origin of fungal isolate (i.e. land use) and their symbiotic performance in cowpea.

Bradyrhizobium brasilense sp. nov., a symbiotic nitrogen-fixing bacterium isolated from Brazilian tropical soils.

Four strains of rhizobia isolated from nodules of Vigna unguiculata (UFLA03-321T, UFLA03-320 and UFLA03-290) and Macroptilium atropurpureum (UFLA04-0212) in Brazilian soils were previously reported as a new group within the genus Bradyrhizobium. To determine their taxonomic position, these strains were characterized in this study using a polyphasic approach. The analysis of the 16S rRNA gene grouped the four strains with Bradyrhizobium pachyrhizi PAC48T. However, the concatenated sequence analysis of the two (recA and glnII) or three (atpD, gyrB and recA) housekeeping genes indicated that these strains represent a novel species of Bradyrhizobium, which is very closely related to B. pachyrhizi PAC48T and B. elkanii USDA 76T. Genomic relatedness analyses between the UFLA03-321T strain and B. elkanii USDA 76T and B. pachyrhizi PAC48T revealed an average nucleotide identity below 96% and values of estimated DNA-DNA hybridization below 70%, confirming that they represent genomically distinct species. Analysis of MALDI-TOF MS (Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry) profiles and phenotypic characteristics also allowed differentiation of the novel species from its two neighboring species. In phylogenetic analysis of nodC and nifH genes, UFLA03-321T exhibited maximum similarity with B. tropiciagri CNPSo 1112T. The data suggest that these four UFLA strains represent a novel species, for which the name Bradyrhizobium brasilense sp. nov. is proposed, with UFLA03-321T (=LMG 29353 =CBAS645) as type strain. G + C content in the DNA of UFLA03-321T is 63.9 mol %.

Native rhizobia from Zn mining soil promote the growth of Leucaena leucocephala on contaminated soil.

Plants on contaminated mining soils often show a reduced growth due to nutrient depletion as well as trace elements (TEs) toxicity. Since those conditions threat plant's survival, plant growth-promoting rhizobacteria (PGPRs), such as rhizobia, might be of crucial importance for plant colonization on TE-contaminated soils. Native rhizobia from mining soils are promising candidates for bioaugmented phytoremediation of those soils as they are adapted to the specific conditions. In this work, rhizobia from Zn- and Cd-contaminated mining soils were in vitro screened for their PGP features [organic acids, indole-3-acetic acid (IAA), and siderophore (SID) production; 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity; and Ca3(PO4)2 solubilization] and Zn and Cd tolerance. In addition, some type and reference rhizobia strains were included in the study as well. The in vitro screening indicated that rhizobia and other native genera have great potential for phytoremediation purposes, by exerting, besides biological N2 fixation, other plant growth-promoting traits. Leucaena leucocephala-Mesorhizobium sp. (UFLA 01-765) showed multielement tolerance and an efficient symbiosis on contaminated soil, decreasing the activities of antioxidative enzymes in shoots. This symbiosis is a promising combination for phytostabilization.

Leguminosae native nodulating bacteria from a gold mine As-contaminated soil: Multi-resistance to trace elements, and possible role in plant growth and mineral nutrition.

Efficient N2-fixing Leguminosae nodulating bacteria resistant to As may facilitate plant growth on As-contaminated sites. In order to identify bacteria holding these features, 24 strains were isolated from nodules of the trap species Crotalaria spectabilis (12) and Stizolobium aterrimum (12) growing on an As-contaminated gold mine site. 16S rRNA gene sequencing revealed that most of the strains belonged to the group of α-Proteobacteria, being representatives of the genera Bradyrhizobium, Rhizobium, Inquilinus, Labrys, Bosea, Starkeya, and Methylobacterium. Strains of the first four genera showed symbiotic efficiency with their original host, and demonstrated in vitro specific plant-growth-promoting (PGP) traits (production of organic acids, indole-3-acetic-acid and siderophores, 1-aminocyclopropane-1-carboxylate deaminase activity, and Ca3(PO4)2 solubilization), and increased resistance to As, Zn, and Cd. In addition, these strains and some type and reference rhizobia strains exhibited a wide resistance spectrum to ß-lactam antibiotics. Both intrinsic PGP abilities and multi-element resistance of rhizobia are promising for exploiting the symbiosis with different legume plants on trace-element-contaminated soils.

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria.

Anthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired-end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.