Effect of Ginkgo biloba leaves on the removal efficiency of Cr(VI) in soil and its underlying mechanism.

Cr(VI) is a toxic, teratogenic, and carcinogenic heavy metal element in soil that poses major ecological and human health risks. In this study, microcosm tests combined with X-ray absorption near-edge spectra (XANES) and 16Sr DNA amplification techniques were used to explore the effect of Ginkgo biloba leaves on the removal efficiency of Cr(VI) in soil and its underlying mechanism. Ginkgo biloba leaves had a favorable remediation effect on soil varying in Cr(VI) contamination levels, and the optimal effect was observed when 5% Ginkgo biloba leaves were added. The occurrence state of Cr(VI) in soil before and after the addition of Ginkgo biloba leaves was analyzed by XANES, which revealed that Cr(VI) was fully converted to the more biologically innocuous Cr(III), and the hydroxyl-containing quercetin in Ginkgo biloba leaves was one of the primary components mediating this reduction reaction. The Cr(VI) content was significantly lower in non-sterilized soil than in sterilized soil, suggesting that soil microorganisms play a key role in the remediation process. The addition of Ginkgo biloba leaves decreased the α-diversity and altered the ß-diversity of the soil bacterial community. Actinobacteria was the dominant phylum in the soil remediated by Ginkgo biloba leaves; four genera of Cr(VI)-reducing bacteria were also enriched, including Agrococcus, Klebsiella, Streptomyces, and Microbacterium. Functional gene abundances predicted by PICRUST indicated that the expression of glutathione synthesis genes was substantially up-regulated, which might be the main metabolic pathway underlying the mitigation of Cr(VI) toxicity in soil by Cr(VI)-reducing bacteria. In sum, Ginkgo biloba leaves can effectively remove soil Cr(VI) and reduce Cr(VI) to Cr(III) via quercetin in soil, which also functions as a carbon source to drive the production of glutathione via Cr(VI)-reducing bacteria and mitigate Cr(VI) toxicity. The findings of this study elucidate the chemical and microbial mechanisms of Cr(VI) removal in soil by Ginkgo biloba leaves and provide insights that could be used to enhance the remediation of Cr(VI)-contaminated soil.

Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication.

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.

Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera.

Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico.

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.

Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae).

Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico.

Marine sediments are an example of one of the most complex microbial habitats. These bacterial communities play an important role in several biogeochemical cycles in the marine ecosystem. In particular, the Gulf of Mexico has a ubiquitous concentration of hydrocarbons in its sediments, representing a very interesting niche to explore. Additionally, the Mexican government has opened its oil industry, offering several exploration and production blocks in shallow and deep water in the southwestern Gulf of Mexico (swGoM), from which there are no public results of conducted studies. Given the higher risk of large-scale oil spills, the design of contingency plans and mitigation activities before oil exploitation is of growing concern. Therefore, a bacterial taxonomic baseline profile is crucial to understanding the impact of any eventual oil spill. Here, we show a genus level taxonomic profile to elucidate the bacterial baseline, pointing out richness and relative abundance, as well as relationships with 79 abiotic parameters, in an area encompassing ∼150,000 km2, including a region where the exploitation of new oil wells has already been authorized. Our results describe for the first time the bacterial landscape of the swGoM, establishing a bacterial baseline "core" of 450 genera for marine sediments in this region. We can also differentiate bacterial populations from shallow and deep zones of the swGoM based on their community structure. Shallow sediments have been chronically exposed to aromatic hydrocarbons, unlike deep zones. Our results reveal that the bacterial community structure is particularly enriched with hydrocarbon-degrading bacteria in the shallow zone, where a greater aromatic hydrocarbon concentration was determined. Differences in the bacterial communities in the swGoM were also observed through a comprehensive comparative analysis relative to various marine sediment sequencing projects, including sampled sites from the Deep Water Horizon oil spill. This study in the swGoM provides clues to the bacterial population adaptation to the ubiquitous presence of hydrocarbons and reveals organisms such as Thioprofundum bacteria with potential applications in ecological surveillance. This resource will allow us to differentiate between natural conditions and alterations generated by oil extraction activities, which, in turn, enables us to assess the environmental impact of such activities.

Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens.

Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.

Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest.

Several studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirK and nirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances. Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria were the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCE Understanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.(AU)

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

Abstract In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula.

Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100-502 m total depth) and the adjacent North Bransfield Basin (693-1147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

Nitrogen transforming bacteria within a full-scale partially saturated vertical subsurface flow constructed wetland treating urban wastewater.

The aim of this study was to characterize the nitrogen transforming bacterial communities within a partially saturated vertical subsurface flow constructed wetland (VF) treating urban wastewater in southern Brazil. The VF had a surface area of 3144m2, and was divided into four wetland cells, out of which two were operated while the other two rested, alternating cycles of 30days. The nitrifying and denitrifying bacterial communities were characterized in wetland cell 3 (764m2 surface area) over a period of 12months by using the FISH technique. Samples were collected monthly (from Feb 2014 to Feb 2015) from different layers within the vertical profile, during operation and rest periods, comprising a total of 6 sampling campaigns while the cell was in operation and another 6 when the cell was at rest. This wetland cell operated with an average organic loading rate (OLR) of 4gCODm-2d-1 and a hydraulic loading rate of 24.5mmd-1. The rest periods of the wetland cell presented influences on the abundance of ammonia-oxidizing bacteria (AOB) (8% and 3% for feed and rest periods, respectively), and nitrite-oxidizing bacteria (NOB) (5% and 2% for feed and rest periods, respectively). However, there was no influence of the rest periods on the denitrifying bacteria. AOB were only identified in the top layer (AOB ß-proteobacteria) in both operational and rest periods. On the other hand, the NOB (Nistrospirae and Nitrospina gracilis) were identified in feed periods just in the top layer and during rest periods just in the intermediate layer. The denitrifying bacteria (Pseudomonas spp. and Thiobacillus denitrificans) were identified from the intermediate layer downwards, and remained stable in both periods. Based on the identified bacterial dynamics, the partially saturated VF wetland operated under low OLR enabled favorable conditions for simultaneous nitrification and denitrification.

Bacterial indicator taxa in soils under different long-term agricultural management.

AIMS: In this study, the species indicator test was used to identify key bacterial taxa affected by changes in the soil environment as a result of conservation agriculture or conventional practices. METHODS AND RESULTS: Soils cultivated with wheat (Triticum spp. L.) and maize (Zea mays L.) under different raised bed planting systems for 20 years, that is, varying crop residue and fertilizer management, were used. Taxonomic- and divergence-based 16S-metagenomics, and IndVal analysis were used to study the bacterial communities and identify indicator taxa (genus and OTU97 ) affected by agricultural practices. Although, some phyla were affected significantly by different treatments, the taxonomic assemblages at phylum level were similar. Bacterial taxa related to different processes of the N-cycle were indicators of different fertilization rates, for example, Azorhizobium, Nostoc and Nitrosomonas. A large number of OTU97 were indicators for conventionally tilled beds and their distribution was defined by soil organic carbon. IndVal analysis identified different taxa in each of the residue management systems. This suggests that although the same organic material remains in the field, crop residue management affects specific taxa. The taxa indicator of the burned residues belonged mainly to the order SBR1031 (Anaerolineae, Chloroflexi), and the genera Bacillus and Alicyclobacillus. CONCLUSIONS: N-fertilizer application rates affected N-cycling taxa. Tillage affected Actinobacteria members and organic matter decomposers. Although the same crop residue was retained in the field, organic material management was important for specific taxa. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, we report that agricultural practice affected soil bacterial communities. We also identified distinctive taxa and related their distribution to changes in the soil environment resulting from different agricultural practices.