Microbial functional diversity

In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approa...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the –in particular functional– diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g. soil fertility and aggregation); climate regulation (e.g. carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and r...

The aim of this study was to assess and to detect factors controlling the temperature sensitivity of soil organic matter (SOM) in boreal forests, constituting an important stock of carbon. Soils were collected under Scots pine, Norway spruce, silver birch and mixed forests (O horizon) in northern Finland and measured for basal respiration rate at five different temperatures (from 4˚C to 28˚C). Q 10 values were calculated using a Gaussian function and based on temperature-dependent changes. The soils were measured for the a range of physicochemical parameters and functional diversity of soil microbial communities was assessed using the novel MicroResp™ method. Temperature sensitivity of SOM decomposition differed under the studied forest stands, with pine forests exhibiting the highest temperature sensitivity of SOM decomposition at a lower temperature range (0°C-12°C). In such temperature range we found that Q 10 values were positively correlated with microbial functional diversity index (H' mic) and soil C-toP ratio. These suggest that metabolic abilities of soil microbial communities and soil nutrient content are the important controls of temperature sensitivity of taiga soils.

Mining and smelting sectors contribute significantly to global growth on a regional and local scale. However, the operations are causing significant environmental damage, particularly pollution of the soil with potentially toxic metals (PTMs).  In this study, the speciation of PTMs (arsenic, cadmium, chromium, mercury, manganese, nickel, lead and zinc) from the mine impacted soils of Riruwai mining area was investigated using a modified Tessier sequential extraction method. The findings of the study revealed that all the PTMs examined are considerably associated with non-residual fractions in all the sampling locations. This indicates that all the PTMs investigated in the study area may be highly mobile in the soils and hence potentially toxic. The concentrations of PTMs in the soil’s geochemical fractions were found to vary with the sampling locations, with active mining sites significantly (p ≤ 0.05) recording the highest value, followed by farmland, while the lowest value was rep...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the –in particular functional– diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g. soil fertility and aggregation); climate regulation (e.g. carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and r...

; ROSA LINA DEFRIERI; GABRIELA CRISTINA SARTI; JHOVANA ESCOBAR ORTEGA & INES GARCÍA DE SALAMONE RESUMEN En los sistemas forestales, la hojarasca es generalmente la principal fuente de nutrientes para la vegetación y microorganismos, pudiendo variar éstos en relación a la biomasa y calidad de los materiales aportados por diferentes especies. Las raíces de los árboles ejercen influencia en el desarrollo y actividad de la microflora. El objetivo de este trabajo fue evaluar la influencia sobre el suelo de dos especies arbóreas implantadas, con distinta composición del residuo vegetal aportado al suelo. El suelo está clasificado como un Andisol y está ubicado en la Estación Forestal Trevelín, Chubut, Argentina, Lat. 43º Sur, Long 71º31´ Oeste. Se extrajeron muestras superficiales de suelo de dos parcelas de bosque con una especie dominante cada una: Pino radiata (Pinus radiata D. Don.) y Roble europeo (Quercus robur). Se determinó carbono orgánico, respiración microbiana, actividad deshidrogenasa, diversidad funcional de comunidades microbianas asociadas y se calculó el índice de diversidad de Shanon Weaver (H). Se cuantificaron bacterias totales, bacterias amilolíticas, actinomicetes y hongos. Los valores de respiración microbiana y carbono orgánico resultaron significativamente superiores en el suelo debajo de Roble. No se encontraron diferencias significativas entre valores de deshidrogenasa. Los recuentos de flora bacteriana total y de bacterias amilolíticas dieron significativamente superiores en el suelo asociado a Roble, mientras que los actinomicetes y hongos no mostraron diferencias significativas entre especies. El análisis de componentes principales mostró variaciones significativas en la fisiología de las comunidades microbianas asociadas a estas dos especies. El índice de diversidad H de la microflora fue significativamente mayor para Pino. Los residuos de Roble por ser una especie latifoliada y por lo tanto poseer menor contenido de sustancias recalcitrantes que una conífera, asociado al mayor desarrollo de bacterias totales y amilolíticas, podría favorecer una mayor descomposición del residuo vegetal aportado al suelo y explicar los mayores valores de carbono orgánico y respiración microbiana obtenidos. Palabras clave. Palabras clave. Palabras clave. Palabras clave. Palabras clave. Suelo forestal, respiración microbiana, actividad deshidrogenada, diversidad funcional microbiana.

The aim of the present study was to determine the effect of two implanted forest species with different vegetal residue chemical compositions on the biological and biochemical properties of soil. The study site was located in the INTA Forestal Station of Trevelin, Chubut, Argentina. Samples were extracted from soil in forest plots dominated by Radiata Pine (Pinus radiata D. Don.) or European Ash (Fraxinus excelsior L.). Microbial respiration, dehydrogenase activity, community-level physiological profile (CLPP) and index of microbial community functional diversity were used as biological parameters; and acid phosphatase, protease and β-glucosidase activities were employed as biochemical parameters. Microbial respiration, dehydrogenase and acid phosphatase activities showed greater values in soil under European Ash trees; however, significant differences in protease and β-glucosidase activities were not observed among species. The higher organic C content of soil under European Ash tr...

In forest systems, leaf litter is usually the main source of nutrients for the vegetation and microorganisms. Leaf litter composition may vary according to the biomass and quality of the materials produced by different species. Tree roots affect the development and activity of ...

Mining and smelting sectors contribute significantly to global growth on a regional and local scale. However, the operations are causing significant environmental damage, particularly pollution of the soil with potentially toxic metals (PTMs).  In this study, the speciation of PTMs (arsenic, cadmium, chromium, mercury, manganese, nickel, lead and zinc) from the mine impacted soils of Riruwai mining area was investigated using a modified Tessier sequential extraction method. The findings of the study revealed that all the PTMs examined are considerably associated with non-residual fractions in all the sampling locations. This indicates that all the PTMs investigated in the study area may be highly mobile in the soils and hence potentially toxic. The concentrations of PTMs in the soil’s geochemical fractions were found to vary with the sampling locations, with active mining sites significantly (p ≤ 0.05) recording the highest value, followed by farmland, while the lowest value was rep...

Mountain forest soils contain an important stock of carbon. Their altitudinal gradient can serve as a model for research on the potential risk of increased emission of carbon dioxide to the atmosphere, in a positive feedback of global warming. Using soil samples collected at three elevations (600, 900, and 1200 m a.s.l.) from five separate slopes of the Carpathian Mountains (Poland), we studied the effects of soil physical, chemical and microbial properties controlling the temperature sensitivity (Q 10 values) of organic matter decomposition in forest soils. Data of soil basal respiration rate measured in laboratory conditions at six different temperatures (5, 10, 15, 20, 25 and 30°C) were fitted to a Gaussian function. The modelled soil respiration rates differed between altitudes at temperature exceeding 15°C, and the respiration rate of soil from 1200 m a.s.l. was higher than in soils from the two lower elevations. Based on the modelled respiration values, we calculated Q 10 values in the low (Q 10 L, 0-10°C), medium (Q 10 M, 10-20°C) and high (Q 10 H, 20-30°C) temperature ranges. The Q 10 values did not differ between elevations. Q 10 L and Q 10 M were negatively related only with the C:N ratio. Temperature sensitivity of decomposition of soil organic matter was not affected by bacterial activity and functional diversity (assessed using Biolog Ò ECO plates), microbial biomass or community structure (inferred from phospholipid fatty acid assays). Our findings support a kinetics-based theory of the higher temperature sensitivity of more chemically recalcitrant soil organic matter, put forward by other authors. Keywords Biolog Ò ECO plates AE CO 2 evolution AE Global warming AE Microbial functional diversity AE Phospholipid fatty acids (PLFA)

These researches fit into the works coordinated by the Observatoire Hommes-Milieux (OHM) of Bassin Minier de Provence (BMP) and dedicated to vegetal covers and microbial communities of soils. They aim to study the terrestrial deposits of red muds resulting from past and current activities of alumina extraction. Despite the red muds have been extensively studied about their industrial recycling potentials (Klauber et al., 2011), the studies on their environmental effects, especially on the biological component of soils, are far less numerous (Garau et al., 2007, 2011, 2014; Krishna et al., 2014; Lombi et al., 2002) and, furthermore, lacking in the context of BMP. To this date, the various studies available in the literature emphasize the importance of the soil matrix in the modulation of biological responses when it is mixed with red muds. Therefore, this aspect is important to invest at the local scale in the prospect of a potential use of red muds as improvement to soils or to the ...

These researches fit into the works coordinated by the Observatoire Hommes-Milieux (OHM) of Bassin Minier de Provence (BMP) and dedicated to vegetal covers and microbial communities of soils. They aim to study the terrestrial deposits of red muds resulting from past and current activities of alumina extraction. Despite the red muds have been extensively studied about their industrial recycling potentials (Klauber et al., 2011), the studies on their environmental effects, especially on the biological component of soils, are far less numerous (Garau et al., 2007, 2011, 2014; Krishna et al., 2014; Lombi et al., 2002) and, furthermore, lacking in the context of BMP. To this date, the various studies available in the literature emphasize the importance of the soil matrix in the modulation of biological responses when it is mixed with red muds. Therefore, this aspect is important to invest at the local scale in the prospect of a potential use of red muds as improvement to soils or to the ...

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (470%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the-in particular functional-diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g., soil fertility and aggregation); climate regulation (e.g., carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and reduction of contaminant-related hazards for human health. We also consider how microbial trait-based approaches can be used as a tool to improve cultivated plant performance through artificial selection and microbiome engineering. Last, we discuss the inherent obstacles associated with the development and implementation of trait-based approaches owing to strong interactions within microbial communities and linkages between plants and the soil environment. Despite these obstacles, microbial trait-based approaches hold promise for the sustainable management of agricultural ecosystems needed to feed and nourish a rapidly growing human population.

Taxon-specific traits/multiple traits in individual taxa/tradeoffs among traits Key eco-physiological techniques Stable isotope probing; Biolog/Ecoplates; etc. Metabolic and physiological studies of individual cells and strains Key-omics techniques DNA and RNA single gene sequence diversity; environmental (meta-)genomics, transcriptomics, proteomics, and metabolomics Genomics, transcriptomics, proteomics, and metabolomics on cells and strains Main scale The real world (field studies; complex natural communities) Laboratory (model systems)

Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral Acropora digitifera from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to eggsperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.

Coral restoration is important in ocean engineering because corals play a crucial role for sustainable marine ecosystems and in global carbon cycle. Coral microbiome controls the host life and functions by occupying different coral components such as tissue, skeleton, mucus and surrounding water. They work together as a complementary community to create the circle of healthy life for coral reefs. In addition to their role in carbon, nitrogen and sulfur cycling, metabolism and defence, their pattern of abundance and diversity shapes coral resilience and adaptation to the changing environment. As coral reefs are facing a tremendous decline by climate change and human activities, we here review the motors shifting the pattern of natural coral microbiome, and how this microbiome shift could affect coral health or drive coral adaptation to both climate change and anthropogenic disturbances. The available coral restoration techniques and their limitations are also discussed, particularly the new arising trend of coral restoration through coral microbiome. After presenting the high value of microbial community in maintaining coral reef health, we suggest that coral restoration through their microbiome could be a self-sustaining tool in fighting worldwide coral decline and urge scientist to draw more attention toward this new approach.

Viterbo area is naturally polluted with arsenic (As) as a result of geochemical mobilization of this metalloid through hydrothermal processes that lead to the up-flow of thermal waters. The area is characterised by thermal springs with arsenic concentrations ranging from 180 to 370 μgL -1 and the soils are calcareous. Soil samples were taken in the area surrounding Bullicame hot springs and inside the nearby University Botanical Gardens with the aim to assess: i) the distribution and bioavailability of arsenic in the soil, ii) the effect of plant cover on its distribution and iii) microbial functional diversity. The sampling points were then the Control (near the thermal springs), Pinus halepensis, Quercus spp., Mediterranean maquis and anot-planted area all found within theBotanical gardens. The results reflected a considerable amount of arsenic associated to the CaCO 3 fraction which may become unstable under changing environmental conditions thus potentially hazardous. The presence of different plant covers affects the arsenic content in the soil differently as was evident in the drastic reduction of As content under conifer plants (Pinus halepensis) cover. The presence of plant products favours a higher functional diversity of microbial processes as opposed to the drastic reduction in microbial functional diversity observed in the control site where the CaCO 3 content is elevated and no vegetation is present. These preliminary results offer an interesting opportunity to study the complex interactions of this toxic metalloid in a soil-plant system in a naturally polluted environment.

Temperature sensitivity of community-level physiological profiles (CLPPs) was examined for two semiarid soils from the southwestern United States using five different C-substrate profile microtiter plates (Biolog GN2, GP2, ECO, SFN2, and SFP2) incubated at five different temperature regimes. The CLPPs produced from all plate types were relatively unaffected by these contrasting incubation temperature regimes. Our results demonstrate the ability to detect CLPP differences between similar soils with differing physiological parameters, and these differences are relatively insensitive to incubation temperature. Our study also highlights the importance of using both bacterial and fungal plate types when investigating microbial community differences by CLPP. Nevertheless, it is unclear whether or not the differences in CLPPs generated using these plates reflect actual functional differences in the microbial communities from these soils in situ.

Taxon-specific traits/multiple traits in individual taxa/tradeoffs among traits Key eco-physiological techniques Stable isotope probing; Biolog/Ecoplates; etc. Metabolic and physiological studies of individual cells and strains Key-omics techniques DNA and RNA single gene sequence diversity; environmental (meta-)genomics, transcriptomics, proteomics, and metabolomics Genomics, transcriptomics, proteomics, and metabolomics on cells and strains Main scale The real world (field studies; complex natural communities) Laboratory (model systems)

The majority of biomass in the McMurdo Dry Valleys of Antarctica occurs within rocks and soils, but despite the wealth of biodiversity data very little is known about the potential functionality of communities within these substrates. The putative physiological capacity of microbial communities in granite boulders (chasmoendoliths) and soils of a maritime-influenced Antarctic Dry Valleys were interrogated using the GeoChip microarray. Diversity estimates revealed surprisingly high diversity and evenness in both communities, with Chlorobi and Deinococci in soils accounting for major differences between the substrates. Autotrophs were more diverse in chasmoendoliths, and diazotrophs more diverse in soils. Both substrates revealed a previously unappreciated abundance of Halobacteria (Archaea), Ascomycota (Fungi) and Basidiomycoyta (Fungi). The fungi accounted for much of the differences between substrates in metabolic pathways associated with carbon transformations, particularly for aromatic compounds. Nitrogen fixation genes were more common in soils, although nitrogen catabolism genes were abundant in chasmoendoliths. Stress response pathways were more diverse in chasmoendoliths, possibly reflecting greater environmental stress in this exposed substrate compared with subsurface soils. Overall diversity of stresstolerance genes was markedly lower than that recorded for inland locations where environmental stress is exacerbated. We postulate that the chasmoendolithic community occupies a key role in biogeochemical transformations in Dry Valley systems where granite substrates are abundant among open soils. The findings indicate that a substantial upward revision to estimates of biologically active surfaces in this system is warranted.

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth's canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this relationship is influenced by environmental gradients. The proposed project focuses on decomposition as one of the most important microbial soil ecosystem functions.

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth's canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this relationship is influenced by environmental gradients. The proposed project focuses on decomposition as one of the most important microbial soil ecosystem functions.

Taxon-specific traits/multiple traits in individual taxa/tradeoffs among traits Key eco-physiological techniques Stable isotope probing; Biolog/Ecoplates; etc. Metabolic and physiological studies of individual cells and strains Key-omics techniques DNA and RNA single gene sequence diversity; environmental (meta-)genomics, transcriptomics, proteomics, and metabolomics Genomics, transcriptomics, proteomics, and metabolomics on cells and strains Main scale The real world (field studies; complex natural communities) Laboratory (model systems)

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth’s canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this rel...

A lacuna exists in our understanding of the genetic makeup of bacteria, due to scarcity of genome sequences. We report here the first draft genome sequence of  Acr-14, a type strain isolated from the coral This sequence will foster an understanding of the genetic makeup and role of hosts in shaping gene repertoires.

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (470%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

We report here the draft genome sequences of Sphingomonas sp. IBVSS1 and IBVSS2, two bacteria assembled from the metagenomes of surface samples from freshwater lakes. The genomes are 99% complete and may represent new species within the Sphingomonas genus, indicating a larger diversity than currently identified .

We report here the draft genome sequences of Hydrogenophaga sp. strains IBVHS1 and IBVHS2, two bacteria assembled from the metagenomes of surface samples from freshwater lakes. The genomes are 95% complete and may represent new species within the Hydrogenophaga genus, indicating a larger diversity than currently identified.

In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.

Arsenic Availability And Microbial Functional Diversity As Influenced By Different Plant Covers In Calcareous Soils Of Central Italy

Abstract

Viterbo is naturally polluted with arsenic as a result of geo-chemical mobilization through hydro-thermal processes that lead to the up flow of thermals waters. The area is characterized by thermal springs with arsenic concentrations ranging from 180 to 370 μg L-1. and the soils are calcareous. 5 samples were analysed chemically and biochemically to assess the distribution and bio-availability of arsenic in the soil, the effect of plant cover on its distribution and the functional diversity in response to arsenic. The sampling points were the control (near the thermal springs), Pinus halepensis, Quercus spp., Mediterranean maquis and the not-planted areas all found in botanical gardens of the University of Tuscia. The results reflected a considerable amount of arsenic associated to the CaCO3 fraction which may become unstable under changing environmental conditions. The presence of different plant covers affects the arsenic content in the soil differently as was evident in the drastic reduction of As content in the conifer plant (Pinus halepensis) cover. The presence of plant products favours a higher functional diversity of microbial processes as opposed to the drastic reduction in microbial functional diversity observed in the control site where there CaCO3 content is elevated and there are not plants.

Keywords: Arsenic, calcareous soils, bio-availability, plant uptake, functional diversity