Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance

Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado

Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

Assessment of soil bacterial communities in integrated crop production systems within the Amazon Biome, Brazil: a comparative study

Integrated production systems have been proposed as alternative to sustainable land use. However, information regarding bacterial community structure and diversity in soils of integrated Crop-Livestock-Forest systems remains unknown. We hypothesize that these integrated production systems, with their ecological intensification, can modulate the soil bacterial communities. However, Yet, it remains unclear whether the modulation of bacterial biodiversity is solely attributable to the complexity of root exudates or if seasonal climatic events also play a contributory role. The objective of this study is to evaluate the impact of monoculture and integrated production systems on bacterial soil communities in the Amazon Biome, Brazil. Three monoculture systems, each with a single crop over time and space (Eucalyptus (E), Crop Soybean (C), Pasture (P)), and three integrated systems with multiple crops over time and space (ECI, PI, ECPI) were evaluated, along with a Native forest serving as a reference area. Soil samples were collected at a depth of 0-10 cm during both the wet and dry seasons. Bacterial composition was determined using Illumina high-throughput sequencing of the 16 S rRNA gene. The sequencing results revealed the highest abundance classified under the phyla Firmicutes, Actinobacteria, and Proteobacteria. The Firmicutes correlated with the Crop in the rainy period and in the dry only ECPI and Forest. For five classes corresponding to the three phyla, the Crop stood out with the greatest fluctuations in their relative abundance compared to other production systems. In cluster analysis by genus during the rainy season, only Forest and ECPI showed no similarity with the other production systems. However, in the dry season, both were grouped with Forest and EPI. Therefore, the bacterial community in integrated systems proved to be sensitive to management practices, even with only two years of use. ECPI demonstrated the greatest similarity in bacterial structure to the Native forest, despite just two years of experimental deployment. Crop exhibited fluctuations in relative abundance in both seasons, indicating an unsustainable production system with changes in soil microbial composition. These findings support our hypothesis that integrated production systems and their ecological intensification, as exemplified by ECPI, can indeed modulate soil bacterial communities.

Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis

One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.

Insights into taxonomic diversity and bioprospecting potential of Cerrado endophytic fungi: a review exploring an unique Brazilian biome and methodological limitations

Cerrado is the second largest biome in Brazil, and it is known for harboring a wide variety of endemic plant and microbial species, among which are endophytic fungi. Endophytic fungi are microorganisms capable of colonizing the interior of plant tissues without causing disease in host plants. Especially in the Cerrado biome, this group of microorganisms is still poorly studied and information on species estimation, ecological and evolutionary importance is not accurate and remains unknown. Also, it is extremely important to emphasize that great part of studies available on Cerrado endophytic fungi are national literature, including master's dissertations, course conclusion works or unpublished doctoral theses. The majority of these studies has highlighted that the endemic plant species are an important habitat for fungal endophytes, and new species have increasingly been described. Due to the lack of international literature on Cerrado endophytic fungi, the present review brings a bibliographic survey on taxonomic diversity and bioprospecting potential of fungal endophytes from a unique environment. This review also emphasizes the importance of studying Brazilian endophytic fungi from Cerrado as a source of new technologies (biofertilizer and biocontroller), since they are secondary metabolite-producing organisms with different biological activities for biotechnological, agricultural and pharmaceutical applications.

Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland

The land-use change from natural to managed farmland ecosystems can undergo perturbations and significantly impact soil environment and communities. To understand how anthropogenic land-use alteration determines in-depth relationships among soil environmental factors and soil bacterial communities, high-resolution characterization was performed using soil samples (27 spots × 3 depths; top 10-20 cm, middle 90-100 cm, bottom 180-190 cm) from a natural forest and a 50 year-old farmland. The soil bacterial community abundance (number of OTU's per sample) and diversity (Faith's phylogenetic diversity) was significantly higher in the top layer of farmland soil than in forest soil. However, the differences in bacterial community abundance between farmland and forest decreased with depth, suggesting that the effect of fertilization was limited to top and middle layers. The phyla Acidobacteria and Proteobacteria were distributed distinctively during the land-use change. The subgroups Gp1-3 of Acidobacteria were more abundant in the forest samples (pH 3.5-5), while Gp4-7 and Gp10 were predominant in the farmland (pH 4.5-9.5). Members belonging to α-Proteobacteria and Xanthomonadales in γ-Proteobacteria were dominant in the forest, whereas β-, δ-, and γ-Proteobacteria were relatively abundant in the farmland. Both multivariate and correlation network analyses revealed that Acidobacteria and Proteobacteria communities were significantly affected by soil pH, as well as toxic metals from pesticides (Zn, Cr, Ni, Cu, Cd, As) and terminal electron acceptors (NO₃, bioavailable Fe(III), SO₄). In line with the long history of anthropogenic fertilization, the farmland site showed high abundance of membrane and ATP-binding cassette transporter genes, suggesting the key for uptake of nutrients and for protection against toxic metals and environmental stresses. This study provides new insights into the use of both Acidobacteria and Proteobacteria community structures as a bacterial indicator for land-use change.

Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils

The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire

Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.

Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study

The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.

The profile of the soil microbiota in the Cerrado is influenced by land use

Extensive areas of the Cerrado biome have been deforested by the rapid advance of agricultural frontiers, especially by agricultural monocultures, and cultivated pastures. The objective of this study was to characterize the soil microbial community of an environment without anthropogenic interference and to compare it with soybean soil and pasture areas. For that, metagenomic sequencing techniques of the 16S rRNA gene were employed. Consistent changes in the profiles of diversity and abundance were described between communities in relation to the type of soil. The soil microbiome of the native environment was influenced by the pH level and content of Al³⁺, whereas the soil microbiomes cultivated with soybean and pasture were associated with the levels of nutrients N and P and the ions Ca²⁺ and Mg²⁺, respectively. The analysis of bacterial communities in the soil of the native environment showed a high abundance of members of the Proteobacteria phylum, with emphasis on the Bradyrhizobium and Burkholderia genera. In addition, significant levels of species of the Bacillus genus, and Dyella ginsengisoli, and Edaphobacter aggregans of the Acidobacteria phylum were detected. In the soil community with soybean cultivation, there was a predominance of Proteobacteria, mainly of the Sphingobium and Sphingomonas genera. In the pasture, the soil microbiota was dominated by the Firmicutes, which was almost entirely represented by the Bacillus genus. These results suggest an adaptation of the bacterial community to the soybean and pasture cultivations and will support understanding how environmental and anthropogenic factors shape the soil microbial community. KEY POINTS: • The Cerrado soil microbiota is sensitive to impacts on the biome. • Microbial communities have been altered at all taxonomic levels.

Seasonal and long-term effects of nutrient additions and liming on the nifH gene in cerrado soils under native vegetation

Biological nitrogen fixation (BNF) represents the main input source of N in tropical savannas. BNF could be particularly important for Brazilian savannas (known as Cerrado) that show a highly conservative N cycle. We evaluated the effects of seasonal precipitation and nutrient additions on the nifH gene abundance in soils from a long-term fertilization experiment in a Cerrado's native area. The experiment consists of five treatments: (1) control, (2) liming, (3) nitrogen (N), (4) nitrogen + phosphorus (NP), and (5) phosphorus (P) additions. The nifH gene sequence was related to Bradyrhizobium members. Seasonal effects on N-fixing potential were observed by a decrease in the nifH relative abundance from rainy to dry season in control, N, and NP treatments. A significant reduction in nifH abundance was found in the liming treatment in both seasons. The findings evidenced the multiple factors controlling the potential N-fixing by free-living diazotrophs in these nutrient-limited and seasonally dry ecosystems.

Beneficial Plant-Associated Microorganisms From Semiarid Regions and Seasonally Dry Environments: A Review

Semiarid regions are apparently low biodiversity environments; however, these environments may host a phylogenetically diverse microbial community associated with plants. Their microbial inhabitants are often recruited to withstand stressful settings and improve plant growth under harsh conditions. Thus, plant-associated microorganisms isolated from semiarid and seasonally dry environments will be detailed in the present review, focusing on plant growth promotion potential and the microbial ability to alleviate plant abiotic stress. Initially, we explored the role of microbes from dry environments around the world, and then, we focused on seasonally dry Brazilian biomes, the Caatinga and the Cerrado. Cultivable bacteria from semiarid and seasonally dry environments have demonstrated great plant growth promotion traits such as plant hormone production, mobilization of insoluble nutrients, and mechanisms related to plant abiotic stress alleviation. Several of these isolates were able to improve plant growth under stressful conditions commonly present in typical semiarid regions, such as high salinity and drought. Additionally, we highlight the potential of plants highly adapted to seasonal climates from the Caatinga and Cerrado biomes as a suitable pool of microbial inoculants to maintain plant growth under abiotic stress conditions. In general, we point out the potential for the exploitation of new microbial inoculants from plants growing in dry environments to ensure a sustainable increase in agricultural productivity in a future climate change scenario.

Effects of aging and transformation of anatase and rutile TiO2 nanoparticles on biological phosphorus removal in sequencing batch reactors and related toxic mechanisms

The effect of nanomaterials aging, namely the transformation of comprehensive characteristics after experiencing real or complex environmental behaviors, on their ecotoxicology is still lacking. Moreover, the mechanisms by which NPs influence biological phosphorus (P) removal during sewage treatment require further elucidation. Therefore, we used both pristine and aged anatase (TiO₂-A) and rutile (TiO₂-R) NPs to investigate the mechanisms by which NPs affect P removal in a SBR. At 0.1 mg/L, the four types of NPs (pristine and aged) had no significant effect on sludge purification after acute (72-h) exposure under simulated sunlight. However, at 50 mg/L-regardless of the crystalline phase of the NPs-SOP and COD removal efficiency dropped steeply to approximately 42.2-82.4 % (p < 0.05) and 69.8-83.3 % (p < 0.05), respectively, especially in the pristine TiO₂-NPs groups because of decrease of richness and diversity of genus level of PAOs and enzyme activity of both PPK and PPX, and the sluggish transformation of PHA and glycogen. Aging reduced the ability of NPs toxicity. The toxicity mechanisms of TiO₂-NPs included lipid peroxidation and contact damage, or leakage from bacterial cytoplasmic membrane, which are closely related to photooxidation capacity and aqueous solution stability-i.e., nanoscale effects-and the impacts of aging or inclusion.

Seasonal Variations in Soil Microbiota Profile of Termite (Syntermes wheeleri) Mounds in the Brazilian Tropical Savanna

Eusocial animals, such as the termites, often build a nest-like structure called a mound that provides shelter with stable internal conditions and protection against predators. Termites are important components of the Brazilian Cerrado biota. This study aimed to investigate the bacterial community composition and diversity of the Syntermes wheeleri termite-mound soil using culture-independent approaches. We considered the vertical profile by comparing two different mound depths (mound surface and 60 cm) and seasonality with samplings during the rainy and dry seasons. We compared the mound soil microbiota to the adjacent soil without the influence of the mound to test the hypothesis that the Cerrado soil bacterial community was more diverse and more susceptible to seasonality than the mound soil microbiota. The results support the hypothesis that the Cerrado soil bacterial community is more diverse than the mound soil and also has a higher variability among seasons. The number of observed OTUs (Operational Taxonomic Units) was used to express bacterial richness, and it indicates that soil moisture has an effect on the community distribution and richness of the Cerrado samples in comparison to mound samples, which remain stable across seasons. This could be a consequence of the protective role of the mound for the termite colony. The overall community taxonomic profile was similar between soil samples, especially when compared to the taxonomic composition of the Syntermes wheeleri termite’s gut, which might be explained by the different characteristics and functionality between the soil and the gut microbial community.

Soil microbial community, enzyme activity, C and N stocks and soil aggregation as affected by land use and soil depth in a tropical climate region of Brazil

The impact of agricultural land-use on soil microbial community composition and enzyme activity has not been extensively investigated in Ultisols. We investigated soil health parameters by analyzing phospholipid fatty acids (PLFAs), extracellular enzyme activity, C and N stocks, and soil structure. Four land uses were established in a tropical climate region of Brazil: native Cerrado (savanna), monoculture pasture [Urochloa brizantha (Hochst. Ex A. Rich.) R. Webster 'Marandu'], an integrated crop-livestock system (ICLS), and maize (Zea mays)-fallow in a no-tillage system. Soil microbial biomass was 40% higher in the native Cerrado than in the monoculture pasture, ICLS, and no-tillage maize. Soil organic carbon was positively correlated with microbial community composition (MB; gram-; AC; AMF; Fungi; F: B ratio) and enzyme activity (bG, AP, NAG). Large macroaggregates were positively correlated with bG, AP, and AMF. In summary, the native Cerrado had a higher level of carbon at the soil surface and greater soil structure with increased microbial biomass, gram+ bacteria, AMF, fungi, and F:B ratio in a tropical region of Brazil. However, bG and AP enzyme activities were lower in the ICLS and no-till maize at the soil surface (0-5 cm) compared to the native Cerrado. The conversion of native Cerrado to agricultural systems shifted the soil microbial community composition, enzyme activity, C and N, and soil structure of this sandy soil of the Brazilian Cerrado.

Soil bacterial community structure of mixed bamboo and broad-leaved forest based on tree crown width ratio

Moso bamboo (Phyllostachysheterocycla (Carr.) Mitford cv. Pubescens) is an economically valuable plant in bamboo production areas of southern China, for which the management mode is crucial for improving the comprehensive benefits of bamboo forest stands. In this respect, mixed forested areas of bamboo and broad-leaved tree species can provide sound ecological management of bamboo in forestry operations. To further this goal, an outstanding question is to better understand the spatial distribution of soil bacterial communities in relation to the proportion of mixed in bamboo and broad-leaved forest. We analyzed soil bacterial community diversity and composition along a proportional gradient of 0–40% mixed-ratio (as represented by the width and size of the broad-leaved tree crown over the plot area) of bamboo and broad-leaved forest in Tianbao Yan Nature Reserve using the highthroughputsequencing of the 16S rRNA gene.Specifically, the sampling plots for the mixed proportions were divided according to the percentage of summed projected area of live broadleaf tree crowns. The main broad-leaved species in the five mixed ratio plots are the same. Each plot was 20 m × 20 m in size, and a total of 15 plots were established, three per forest ratio class. From each plot, soil samples were taken at the surface (0–10 cm depth) in December 2017. Our analysis revealed that soil bacterial diversity community structure and dominant flora changed under different mixing ratios of bamboo and broad-leaved trees. In the stand with a mixed ratio of 10–20%, the bacterial diversity index is higher; however, the diversity was lowest in the 20–30% stands. Among the 20–30% forest soil, Acidobacteria (Solibacteria, Solibacteriales, Acidobacteriales) was more abundant than in soils from other mixed-ratio stands.Redundancy analysis showed that mixed forest stand structure, soil pH, organic carbon, total nitrogen, and soil moisture all contributed to shaping the bacterial community structure. Changes in microbial communities were associated with species diversity in tree layers, availability of soil nutrients (SOC and TN), and changes in soil physical properties (MS, pH). Together, these empirical results suggest that different mixing ratios in the bamboo–broad-leaved mixed forest could influence the soil bacterial community structure indirectly, specifically by affecting the soil physical and chemical properties of the forest.

Bacterial Community Changes Associated with Land Use Type in the Forest Montane Region of Northeast China

Soil microorganisms play a vital role in the biogeochemical cycle, whereas land use change is one of the primary factors that affects the biodiversity and functionality of terrestrial ecosystems. The composition and diversity of bacterial communities (by high-throughput sequencing of the bacterial 16S rRNA gene) were evaluated in the soils of the Montane Region of Northeast China, across different land use types, e.g., natural secondary forest (Quercus mongolica, QM), shrubland (SL), coniferous plantation (Larix gmelinii, LG, and Pinus koraiensis, PK), and agricultural land (Zea mays, ZM). Significant differences in the chemical characteristics and bacterial communities in soils under different land uses were observed in this study. Soil resident TC (total carbon) and TN (total nitrogen) were much higher in secondary natural forest soils, than in coniferous plantation and agricultural soils. Compared with forest and shrubland soils, soil bacterial OTUs, the Chao1 index, and the ACE index were the lowest in the ZM. There were high proportions of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Saccharibacteria, and Nitrospirae in agricultural and forest soils, which accounted for over 90% of the reads in each sample. We found that the dominant group in the forest and shrubland soils was Proteobacteria, while the most dominant group in the ZM was Actinobacteria. The results of both heatmap and principal component analyses displayed groups according to land use types, which indicated that the bacterial communities in the areas under study were significantly influenced by long term differently managed land use. Furthermore, redundancy and Pearson correlation analyses revealed that the bacterial communities were primarily regulated by soil characteristics. This suggested that altered land use patterns initiated changes in the chemical properties of the soils, which affected the composition of microbial communities in this area. This provides a scientific basis for the evolutionary mechanism of soil quality, as well as the rational development and utilization of land resources.

Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas

Changes in soil bacterial communities, which are crucial for the assessment of ecological restoration in Chinese plantations, have never been studied in the "Three North Shelterbelt" project in the semi-arid areas. We used high-throughput sequencing of the 16S rDNA gene to investigate the soil bacterial community diversity, structure, and functional characteristics in three plantation forests, including Populus × canadensis Moench (PC), Pinus sylvestris var. mongolica (PS), and Pinus tabuliformis (PT). In addition, soil environment factors were measured. There were distinct differences in soil characteristics among different plantation forests. Compared to PS and PT, PC had a higher soil pH, dissolved organic carbon (DOC), and available P, as well as a lower C/N ratio. Furthermore, afforestation with different tree species significantly altered the abundance of Proteobacteria, and Chloroflexi in the soil, and its influence on the bacterial diversity indices. The bacterial community compositions and functional groups related to C and N cycling from PS, and PT were grouped tightly, indicating that the soil bacterial phylogenetic distance of PS and PT were closer than that between PS plus PT and PC. Our results implied that the soil characteristics, as well as the diversity, compositions and functions related to C and N cycling of soil bacterial community obviously differed from the following afforestation, especially between PC and PS plus PT, which in turn enormously established the correlation between the soil microbial community characteristics and the afforestation tree species.

The pyrethroid (±)-lambda-cyhalothrin enantioselective biodegradation by a bacterial consortium

Chiral pesticides have been used in agriculture, including (±)-lambda-cyhalothrin ((±)-LC), which is a pyrethroid insecticide widely employed on crops for protection against different types of insects. However, enantioselectivity is poorly studied in biodegradation processes. Therefore, the (±)-LC enantioselective biodegradation by bacteria from Brazilian savannah was reported in this study with a validated analytical method. All bacterial strains biodegraded (±)-LC with different efficiencies. Residual concentrations of LC (3.7-43.1% of biodegradation) and its enantiomeric excesses (0-27% ee) were determined. Additionally, the formation of the main biodegradation metabolite 3-phenoxybenzoic acid was also quantified. A Bacillus consortium composed of the three most efficient strains biodegraded more LC than any isolated strain solely employed in this work, showing that the use of a consortium is an interesting approach. In addition, 13 metabolites were identified and a biodegradation pathway with biochemical reactions of hydrolysis, reduction, esterification, amidation, elimination and group transfer were proposed, confirming the bioremediation potential of these strains. The LC stereoisomer with the highest insecticidal activity (1R,3R,αS-enantiomer, also known as gamma-cyhalothrin) was preferentially biodegraded by the studied bacteria. Therefore, crops protection with gamma-cyhalothrin, which can be applied in lower concentrations than (±)-LC because it is a more effective product against insects, may also be biodegraded faster than the racemic mixture in the environment, decreasing the toxic effects on non-target organisms.

Bacterial diversity in soils of different Hungarian karst areas

Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.

Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange

Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations—a recently logged site that harbored new seedlings and an adult plantation—and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.

Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils

Increased exploitation and use of petroleum resources is leading to increased risk of petroleum contamination of soil and groundwater. Although phytoremediation is a widely-used and cost-effective method for rehabilitating soils polluted by petroleum, bacterial community structure and diversity in soils undergoing phytoremediation is poorly understood. We investigate bacterial community response to phytoremediation in two distinct petroleum-contaminated soils (add prepared petroleum-contaminated soils) from northwest China, Weihe Terrace soil and silty loam from loess tableland. High-throughput sequencing technology was used to compare the bacterial communities in 24 different samples, yielding 18,670 operational taxonomic units (OTUs). The dominant bacterial groups, Proteobacteria (31.92%), Actinobacteria (16.67%), Acidobacteria (13.29%) and Bacteroidetes (6.58%), increased with increasing petroleum concentration from 3000 mg/kg–10,000 mg/kg, while Crenarchaeota (13.58%) and Chloroflexi (4.7%) decreased. At the order level, RB41, Actinomycetales, Cytophagales, envOPS12, Rhodospirillales, MND1 and Xanthomonadales, except Nitrososphaerales, were dominant in Weihe Terrace soil. Bacterial community structure and diversity in the two soils were significantly different at similar petroleum concentrations. In addition, the dominant genera were affected by available nitrogen, which is strongly associated with the plants used for remediation. Overall, the bacterial community structure and diversity were markedly different in the two soils, depending on the species of plants used and the petroleum concentration.

Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado

Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.

Araujo et al. investigate the soil microbiome across four major vegetation zones of the Brazilian Cerrado and find that protist taxon richness increases towards the tree-dominated climax vegetation. Their findings suggest that increased microbiome complexity might enhance system stability towards climax vegetation.

Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem

Lacking sufficient clean water, the paddy soils along the Hengshi River have suffered from long-term acid mine drainage (AMD) contamination. The impacted cropland is too heavily contaminated to grow food safely. The microbial communities inhabiting the environment play pivotal roles in the crop growth, health, and ecological services. In this study, the bacterial, archaeal, and fungal communities in the impacted paddy soil were examined using high-throughput Illumina MiSeq sequencing. The results showed that AMD irrigation considerably enriched the bacterial phylum Acidobacteria and the archaeal phylum Crenarchaeota, while the fungal community was more stable. The abundances of Acidobacteria and Crenarchaeota were significantly positively correlated with the AMD-related environmental factors of pH and heavy metals (Cu, Pb, and Zn). In the most contaminated samples, communities were dominated by the bacteria Candidatus Solibacter and Candidatus Koribacter from the Acidobacteria family. Functional gene profile analysis demonstrated that the energy metabolic processes of the microbial communities, especially C/N related pathways, have adjusted and are well-adapted to tolerating AMD contamination. The present study described the structural and functional differentiation of microbial communities in the rice paddy soil under AMD irrigation. The results are useful for the development of bioremediation strategies using native microbes in the cleanup and biorestoration of AMD-contaminated agriculture soil.

Brazilian Cerrado soil reveals an untapped microbial potential for unpretreated polyethylene biodegradation

Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE's physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas, Delftia, and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes. Considerable nanoroughness shifts and vast damages to the micrometric surface were confirmed by AFM and SEM. Further, phase imaging revealed a 46.7% decrease in the viscous area of biodegraded PE whereas Raman spectroscopy confirmed a loss in its crystalline content, suggesting the assimilation of smaller fragments. Intriguingly, biodegraded PE chemical fingerprint suggests that these strains use novel biochemical strategies in the biodegradation process. Our results indicate that these microbes are capable of degrading unpretreated PE of very high molecular weight (191,000gmol^-1) and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers.

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Elevation gradient of soil bacterial communities in bamboo plantations

BACKGROUND

Elevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan.

RESULTS

Data from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed. Nonmetric multidimensional scaling analysis of the distribution of operational taxonomic units showed differences in bamboo soil bacterial communities across gradients. The bacterial communities at 1000 and 1200 m showed greater diversity than the communities at both lower (600 and 800 m) and higher (1400 and 1800 m) elevations. In contrast to the bacterial community trend, soil C and N and microbial biomass properties increased linearly with elevation.

CONCLUSION

The bamboo soil bacterial community could interact with multiple factors such as soil organic matter content and temperature, for differences in composition and diversity with change in elevation.

Mercury alters the bacterial community structure and diversity in soil even at concentrations lower than the guideline values

This study evaluated the effect of inorganic mercury (Hg) on bacterial community and diversity in different soils. Three soils-neutral, alkaline and acidic-were spiked with six different concentrations of Hg ranging from 0 to 200 mg kg^-1 and aged for 90 days. At the end of the ageing period, 18 samples from three different soils were investigated for bacterial community structure and soil physicochemical properties. Illumina MiSeq-based 16s ribosomal RNA (rRNA) amplicon sequencing revealed the alteration in the bacterial community between un-spiked control soils and Hg-spiked soils. Among the bacterial groups, Actinobacteria (22.65%) were the most abundant phyla in all samples followed by Proteobacteria (21.95%), Bacteroidetes (4.15%), Firmicutes (2.9%) and Acidobacteria (2.04%). However, the largest group showing increased abundance with higher Hg doses was the unclassified group (45.86%), followed by Proteobacteria. Mercury had a considerable negative impact on key soil functional bacteria such as ammonium oxidizers and nitrifiers. Canonical correspondence analysis (CCA) indicated that among the measured soil properties, Hg had a major influence on bacterial community structure. Furthermore, nonlinear regression analysis confirmed that Hg significantly decreased soil bacterial alpha diversity in lower organic carbon containing neutral and alkaline soils, whereas in acidic soil with higher organic carbon there was no significant correlation. EC₂₀ values obtained by a nonlinear regression analysis indicated that Hg significantly decreased soil bacterial diversity in concentrations lower than several guideline values.

Influence of CeO2 NPs on biological phosphorus removal and bacterial community shifts in a sequencing batch biofilm reactor with the differential effects of molecular oxygen

The effects of CeO₂ nanoparticles (CeO₂ NPs) on a sequencing batch biofilm reactor (SBBR) with established biological phosphorus (P) removal were investigated from the processes of anaerobic P release and aerobic P uptake. At low concentration (0.1mg/L), no significant impact was observed on total phosphorus (TP) removal after operating for 8h. However, at a concentration of 20mg/L, TP removal efficiency decreased from 83.68% to 55.88% and 16.76% when the CeO₂ NPs were added at the beginning of the anaerobic and aerobic periods, respectively. Further studies illustrated that the inhibition of the specific P release rate was caused by the reversible states of Ce³⁺ and Ce⁴⁺, which inhibited the activity of exopolyphosphatase (PPX) and transformation of poly-β-hydoxyalkanoates (PHA) and glycogen, as well as the uptake of volatile fatty acids (VFAs). The decrease in the specific P uptake rate was mainly attributed to the significantly suppressed energy generation and decreased abundance of Burkholderia caused by excess reactive oxygen species. The removal of chemical oxygen demand (COD) was not influenced by CeO₂ NPs under aerobic conditions, due to the increased abundance of Acetobacter and Acidocella after exposure. The inhibitory effects of CeO₂ NPs with molecular oxygen were reduced after anaerobic exposure due to the enhanced particle size and the presence of Ce³⁺.

Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20-66%), Chloroflexi (9-29%), and Firmicutes (7-42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43-99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 10⁷ archaeal amoA gene copies g^-1 soil vs. mostly < 7 × 10⁴ bacterial amoA gene copies g^-1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils.

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.

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management.

Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity

There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

BACKGROUND

The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome.

RESULTS

Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance.

CONCLUSION

High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis - contribution to improved aboveground apple plant growth?

Replant disease (RD) severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after 8 weeks was improved in the two RD soils either treated at 50°C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing revealed significant differences in the bacterial community composition even after 8 weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus, and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia, and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e., potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.

Changes of soil bacterial communities in bamboo plantations at different elevations

The effect of altitude on the distribution of plants and animals has been well studied. In contrast, the response of microbes to elevation is poorly understood. To determine whether soil bacterial communities respond to altitudinal gradients, moso bamboo forest soils along a gradient of six elevations from 600 to 1800 m were investigated using the barcoded pyrosequencing method. The results revealed that Acidobacteria and Proteobacteria predominated in the six communities, although the relative abundances were different. Non-metric multidimensional scaling analysis with the abundant OTUs showed that the community composition possessed a complex relationship with elevation. The communities at 1000 and 1200 m were similar and possessed higher levels of diversity than the communities at both lower and higher elevations, giving the diversity a hump-backed trend with elevation. By contrast, the soil C and N and microbial biomass properties increased linearly with elevation. Thus, the complex response of the bacterial community composition and diversity across elevation could not be explained as a simple response to elevation and presumably results from interactions between multiple factors such as soil organic matter content and temperature.

Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna

Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.

Comparison of soil bacterial communities in a natural hardwood forest and coniferous plantations in perhumid subtropical low mountains

BACKGROUND

The bacterial community of forest soils is influenced by environmental disturbance and/or meteorological temperature and precipitation. In this study, we investigated three bacterial communities in soils of a natural hardwood forest and two plantations of conifer, Calocedrus formosana and Cryptomeria japonica, in a perhumid, low mountain area. By comparison with our previous studies with similar temperature and/or precipitation, we aimed to elucidate how disturbance influences the bacterial community in forest soils and whether bacterial communities in similar forest types differ under different climate conditions.

RESULTS

Analysis of 16S ribosomal RNA gene clone libraries revealed that Acidobacteria and Proteobacteria were the most abundant phyla in the three forest soil communities, with similar relative abundance of various bacterial groups. However, UniFrac analysis based on phylogenetic information revealed differences of bacterial communities between natural hardwood forest and coniferous plantation soils. The diversities of bacterial communities of the replanted Calocedrus and Cryptomeria forests were higher than that in natural hardwood forest. The bacterial diversity of these three forest soil were all higher than those in the same forest types at other locations with less precipitation or with lower temperature. In addition, the distribution of some of the most abundant operational taxonomic units in the three communities differed from other forest soils, including those related to Acidobacteria, α-, β- and γ-Proteobacteria.

CONCLUSIONS

Reforestation could increase the bacterial diversity. Therefore, soil bacterial communities could be shaped by the forestry management practices and climate differences in warm and humid conditions.

Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes

16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in "Mata de galeria" forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al(3+) concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored.

Antitumor activity of kielmeyera coriacea leaf constituents in experimental melanoma, tested in vitro and in vivo in syngeneic mice

PURPOSE

The antitumor activity of Kielmeyera coriacea (Clusiaceae), a medicinal plant used in the treatment of parasitic, as well as fungal and bacterial infections by the Brazilian Cerrado population, was investigated.

METHODS

A chloroform extract (CE) of K. coriacea was tested in the murine melanoma cell line (B16F10-Nex2) and a panel of human tumor cell lines. Tumor cell migration was determined by the wound-healing assay and the in vivo antitumor activity of CE was investigated in a melanoma cell metastatic model. 1H NMR and GC/MS were used to determine CE chemical composition.

RESULTS

We found that CE exhibited strong cytotoxic activity against murine melanoma cells and a panel of human tumor cell lines in vitro. CE also inhibited growth of B16F10-Nex2 cells at sub lethal concentrations, inducing cell cycle arrest at S phase, and inhibition of tumor cell migration. Most importantly, administration of CE significantly reduced the number of melanoma metastatic nodules in vivo. Chemical analysis of CE indicated the presence of the long chain fatty compounds, 1-eicosanol, 1-docosanol, and 2-nonadecanone as main constituents.

CONCLUSION

These results indicate that K. coriacea is a promising medicinal plant in cancer therapy exhibiting antitumor activity both in vitro and in vivo against different tumor cell lines.

Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach

Saffron (Crocus sativus L), an autumn-flowering perennial sterile plant, reproduces vegetatively by underground corms. Saffron has biannual corm-root cycle that makes it an interesting candidate to study microbial dynamics in its rhizosphere and cormosphere (area under influence of corm). Culture independent 16S rRNA gene metagenomic study of rhizosphere and cormosphere of Saffron during flowering stage revealed presence of 22 genera but none of the genus was common in all the three samples. Bulk soil bacterial community was represented by 13 genera with Acidobacteria being dominant. In rhizosphere, out of eight different genera identified, Pseudomonas was the most dominant genus. Cormosphere bacteria comprised of six different genera, dominated by the genus Pantoea. This study revealed that the bacterial composition of all the three samples is significantly different (P < 0.05) from each other. This is the first report on the identification of bacteria associated with rhizosphere, cormosphere and bulk soil of Saffron, using cultivation independent 16S rRNA gene targeted metagenomic approach.

Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil

Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas.

Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo

Moso bamboo is fast-growing and negatively allelopathic to neighboring plants. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities. To better understand the impacts of bamboo invasion on soil communities, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation, and bamboo-invaded transition zone were examined using a combination of 16S rRNA gene clone libraries and bar-coded pyrosequencing techniques. Based on the number of operational taxonomic units (OTUs), Shannon diversity index, Chao1 estimator, and rarefaction analysis of both techniques, the bamboo soil bacterial community was the most diverse, followed by the transition zone, with the cedar plantation possessing the lowest diversity. The results from both techniques revealed that the Acidobacteria and Proteobacteria predominated in the three communities, though the relative abundance was different. The 250 most abundant OTUs represented about 70% of the total sequences found by pyrosequencing. Most of these OTUs were found in all three soil communities, demonstrating the overall similarity among the bacterial communities. Nonmetric multidimensional scaling analysis showed further that the bamboo and transition soil communities were more similar with each other than the cedar soils. These results suggest that bamboo invasion to the adjacent cedar plantation gradually increased the bacterial diversity and changed the soil community. In addition, while the 10 most abundant OTUs were distributed worldwide, related sequences were not abundant in soils from outside the forest studied here. This result may be an indication of the uniqueness of this region.