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Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0–10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage β-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.

Published Online: 27 September, 2021, The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known., This work was funded by the Helmholtz Young Investigator grant VH-NG-1248 Micro “Big Data.”, info:eu-repo/semantics/publishedVersion

Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus. Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores., Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems and which degrade the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. In this study, we investigated the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome P450 enzymes and genes in geraniol, cumate, cinnamate, and α-pinene/limonene degradation pathways. Using metatranscriptomic analysis, we showed that some of these degradation genes are expressed in situ. Most of the bacterial isolates grew unhindered in the presence of PSCs and, using gas chromatography-mass spectrometry (GC-MS), we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade α-pinene, β-caryophyllene, or linalool. Using a headspace sampler, we show that subcolonies of fungus gardens reduced α-pinene and linalool over a 36-h period, while L. gongylophorus strains alone reduced only linalool. Overall, our results reveal that the bacterial communities in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system.

Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir Tis study was funded by the project of the Spanish Ministry of Economy and Competitiveness SPACESTREAM (CGL2017-88640-C2-1-R). The authors acknowledge the support from the Economy and Knowledge Department of the Catalan Government through Consolidated Research Group (ICRA-ENV 2017 SGR 1124), and to R. Marcé, D.von Schiller, C. Gutierrez, J. P. Casas-Ruiz, L. Gómez-Gener, V. Acuña and B. Obrador for their help during the sampling. ICRA is part of the CERCA program

Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles “orally healthy” communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.

Temporary streams are characterized by the alternation of dry and wet hydrological phases, creating both a harsh environment for the biota as well as a high diversity of opportunities for adaptation. These systems are mainly microbial-based during several of these hydrological phases, and those growing on all solid substrata (biofilms) accordingly change their physical structure and community composition. Biofilms experience large decreases in cell densities and biomass, both of bacteria and algae, during dryness. Algal and bacterial communities show remarkable decreases in their diversity, at least locally (at the habitat scale). Biofilms also respond with significant physiological plasticity to each of the hydrological changes. The decreasing humidity of the substrata through the drying process, and the changing quantity and quality of organic matter and nutrients available in the stream during that process, causes unequal responses on the biofilm bacteria and algae. Biofilm algae are affected faster than bacteria by the hydric stress, and as a result the ecosystem respiration resists longer than gross primary production to the increasing duration of flow intermittency. This response implies enhancing ecosystem heterotrophy, a pattern that can be exacerbated in temporary streams suffering of longer dry periods under global change This work has received a grant from the European Community 7th Framework Programme undergrant agreement No. 603629-ENV-2013-6.2.1-Globaqua.The authors acknowledge the support from the Economy and Knowledge Department of the Catalan Government as being part of the Consolidated Research Group of the Catalan Institute for Water Research (2014SGR291)

Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO2) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at − 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO2 as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H2 production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 μM min−1) compared to abiotic conditions (5.5 ± 0.6 μM min−1), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis This study has received funding from the European Union’s Horizon 2020 research and innovation program under the grant agreement no 760431. LEQUIA and IEA have been recognized as a consolidated research groups by the Catalan Government (2017-SGR-1552 and 2017SGR-548, respectively). E. P.-V. is grateful for the Research Training grant from the University of Girona (IFUdG2018/52). S.P. is a Serra Hunter Fellow (UdG-AG-575) and acknowledges the funding from the ICREA Academia award

Understanding the drivers of microbiome variation in corals is crucial to better predict the effects of environmental pressures on coral holobionts and coral reef ecosystems. However, much remains to be understood about corals and the interactions they establish with microorganisms. My hypothesis is that the microbiome of the surface mucus layer (SML) is mainly influenced by environmental parameters due to its direct contact with the environment, whereas the tissue microbiome is more driven by the physiology of the coral host. Therefore, the aim of the present work is to distinguish the effect of the host’s intrinsic and environmental factors on the microbiome composition in different coral compartments (SML and tissue), and to identify possible overarching trends in the environmental sensitivity of distinct microbiomes within a coral holobiont. Using next-generation amplicon-sequencing of the 16S rRNA gene, the analyses showed that microbiomes of Acropora spp. differed significantly between compartments (SML versus tissue) and species (A. tenuis versus A. millepora), but also among sampling location and season. Seawater samples were characterized by dominance of members of the Synechococcaceae and Pelagibacteraceae. In Acropora spp., mucus microbiome was dominated by members of Flavobacteriaceae, Synechococcaceae, Rhodobacteraceae and Pelagibacteraceae families, while the tissue microbiome was dominated by the Endozoicimonaceae family. SML microbiomes of both coral hosts correlated best with environmental parameters as ammonium, total suspended solids, particulate organic carbon, number of raindays and nitrate/nitrite. However, the amount of influence from environmental parameters on the mucus (explaining 12-15% of variation) is relatively low as compared with the influence of those parameters on the seawater microbiome (explaining 49% of variation). In contrast, the tissue microbiomes of the two Acropora species showed distinct and species-specific responses to environmental and physiological parameters, suggesting host-specific modulation of the environmental drivers of the tissue microbiome. Os corais são considerados organismos holobiontes, uma unidade viva composta pelo hospedeiro e seu microbioma associado. Os corais, por exemplo, podem estar associados a eucariontes dinoflagelados (família Symbiodiniaceae), procariontes (Bacteria e Archaea) e/ou fungos. Os microrganismos associados aos corais estão envolvidos em diversas funções para o bom funcionamento dos processos fisiológicos do hospedeiro. Por exemplo, podem atuar como mediadores nos ciclos biogeoquímicos e na nutrição do hospedeiro, como também na defesa do mesmo contra agentes patogénicos. Portanto, são essenciais para a manutenção do estado saudável dos corais. Além disso, o microbioma dos corais está sob constante influência de flutuações dos fatores ambientais e fisiológicos dos seus hospedeiros. Compreender os fatores que influenciam a composição e funcionamento do microbioma é crucial para criar estratégias de conservação dos corais e, consequentemente, protegê-los dos efeitos das alterações globais, por exemplo. No entanto, ainda há muito a descobrir sobre a interação simbiótica em corais. O foco da presente tese é a comunidade de procariontes associados, que podem ser referenciados também como comunidades microbianas ou microbiomas ao longo da tese (conforme encontrado na literatura). As comunidades microbianas podem estar associadas a diferentes partes ou “compartimentos” do pólipo do coral. Os compartimentos incluem o muco superficial, tecido, esqueleto e a cavidade gástrovascular. Cada compartimento possui características únicas e, devido a isto, abriga microbiomas específicos, podendo variar tanto em abundância como em diversidade taxonómica. Por exemplo, estudos revelam que o microbioma do muco superficial de pólipos de corais é mais abundante e mais diverso que o tecido interno dos corais. A camada do muco apresenta-se como uma interface entre o epitélio dos pólipos e a coluna de água. Por isso põe-se a hipótese que a sua comunidade microbiana inclui não só os membros já residentes do muco, como também transientes originários de outras fontes (tais como a coluna de água, sedimentos em suspensão e/ou organismos bentónicos). Pelo contrário, as camada de tecido (epiderme e gastroderme) dos corais são dominadas principalmente por bactérias do género Endozoicomonas e também por microalgas fotossintéticas (da família Symbiodinaceae), extremamente importantes para a sobrevivência dos corais. Portanto, o estudo específico do microhabitat que o microbioma habita é crucial para o estudo geral de microbiomas de corais. No entanto, atualmente, estudos que englobam fatores que podem influenciar os microbiomas não se focam em diferentes compartimentos, mas apenas num só compartimento (geralmente o tecido). As primeiras descobertas neste tema mostraram que as comunidades microbianas específicas de corais são relativamente estáveis numa escala espacio-temporal. Estudos mais recentes propõem inúmeros fatores, para além da especificidade, que podem afetar a estrutura e a abundância relativa de membros dos microbiomas de corais. Por exemplo, diferenças geográficas, mudanças sazonais, poluição ou o estado fisiológico do hospedeiro. Porém, este tópico ainda é considerado bastante limitado e controverso, e mais estudos são necessários neste contexto.. O principal objetivo deste estudo é distinguir os efeitos de fatores ambientais e fisiológicos do hospedeiros na variação da composição das comunidades microbianas de diferentes compartimentos nos pólipos de corais (muco e tecido), e também, identificar possíveis tendências da sensibilidade ambiental dos microbiomas identificados. A minha hipótese é que o microbioma do muco é principalmente influenciado por parametros ambientais, devido ao seu contato mais direto com o ambiente, enquanto que o microbioma do tecido responde mais às mudanças fisiológicas do hospedeiro. Para testar esta hipótese, dados de Sequenciamento de Nova Geração (NGS) do gene 16S do RNA ribossomal dos microbiomas de diferentes compartimentos (muco e tecido) e espécies de coral (A. tenuis e A. millepora) foram usados em conjunto com dados de fatores ambientais e fisiológicos dos hospedeiros. O microbioma da coluna de água foi usado como referência no estudo. Em geral, os resultados mostraram que os microbiomas da Acropora diferiram significativamente entre os compartimentos e espécies, e também foram influenciados temporalmente e espacialmente. A riqueza de zOTU (“zero-radius OTU” ou unidade taxonómica operacional, a qual é designada como a menor entidade taxonómica existente) entre os microbiomas analisados diferiu significativamente entre o microbioma do muco, tecido e coluna de água, e também entre as espécies de Acropora. A riqueza de zOTU não diferiu entre estações ou local de coleta. O microbioma da coluna de água abrigou a comunidade mais rica, seguido da do muco e da comunidade do tecido. A diversidade alfa baseada no índex de Shannon também diferiu significativamente entre os microbiomas do muco, tecido e coluna de água, porém não diferiu entre espécies de corais, estação e local de coleta. A diversidade de zOTU foi significativamente maior no microbioma do muco em relação ao microbioma da coluna de água, enquanto que o microbioma do tecido foi o menos diverso entre todos. As amostras da coluna de água foram caracterizadas pela dominância de membros de Synechococcaceae e Pelagibacteraceae. Membros pertencentes às famílias Flavobacteriaceae, Synechococcaceae, Rhodobacteraceae e Pelagibacteraceae foram dominantes no microbioma do muco das espécies de Acropora, e membros da família Endozoicimonaceae foram dominantes no microbioma do tecidos de ambas as espécies. Os microbiomas do muco de ambas espécies de Acropora apresentaram maior influência de parâmetros ambientais como amónia, sólidos suspensos totais, carbono orgânico particulado, número de dias chuvosos e nitritos/nitratos. No entanto, a quantidade de influência dos parâmetros ambientais no muco (explicando 12-15% da variação) é relativamente baixa em comparação com a influência desses parametros no microbioma da água do mar (explicando 49% da variação). Por outro lado, os microbiomas do tecido apresentaram respostas distintas entre as espécies de Acropora nos parâmetros ambientais e fisiológicos, sugerindo modulação específica do hospedeiro aos fatores ambientais do microbioma do tecido. Em conclusão, o presente estudo revela que microbiomas presentes em compartimentos fisicamente distintos respondem diferentemente a fatores ambientais e fisiológicos, o que é uma novidade para os estudos de microbiomas de corais e sua dinâmica. Portanto, este estudo esclarece parte do conhecimento limitado e controverso neste contexto, e também estimula o uso de abordagens metodológicas mais holísticas sobre o tema. Sugestões para estudos futuros podem incluir o uso de outras espécies, diferentes das usadas no presente trabalho, e também testes experimentais (não só baseado em correlações) para o fornecimento de uma compreensão mais ampla da variação de microbiomas em corais.

Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community composition. Strikingly, we found that in comparison to the drying phase, water return (as sporadic storms and rewetting) led to larger shifts in the surface microbial community composition and diversity. In addition, microhabitat characteristics, such as the greater capacity of the hyporheic zone to maintain/conserve moisture, tended to modulate the ability of certain microbes (e.g., bacteria) to cope with severe hydrological disturbances Giulia Gionchetta was awarded a grant (UdG 2016) from the University of Girona. This study was supported by the Spanish Ministry of Economy and Competitiveness through the project FUNSTREAM (CGL2014-58760-C3-R); by the Economy and Knowledge Department of the Catalan Government, through Grant/Award Number: 2014 SGR 484; and through the Short-Term Scientific Mission (STSM) Grant awarded by the Science and Management of Intermittent Rivers and Ephemeral Streams (SMIRES) Cost-Action (Action number: 40271). This study was also partially supported by project BIGLY (ANR-16-CE32-0001) and the project DryHarshSal (RTI2018-097950-B-C21) of the Spanish Ministry of Science, Innovation and Universities

Background The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi. Results The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization. Conclusions The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies. Electronic supplementary material The online version of this article (10.1186/s40168-018-0528-y) contains supplementary material, which is available to authorized users.

1. Microbial heterotrophic activity is a major driver of nutrient and organic matter processing in the hyporheic zone of headwater streams. Additionally, the hypor‐ heic zone might provide refuge for microbes when surface flow ceases during drought events. 2. We investigated chemical (organic and inorganic nutrients) and microbiological parameters (bacterial cell concentration, live–dead ratios, and extracellular en‐ zyme activities) of surface and interstitial pore water in a period of progressive surface-hyporheic disconnection due to summer drying. The special situation of the chosen study reach, where groundwater mixing is impeded by the bedrock forming a natural channel filled with sediment, allowed as to study the transfor‐ mation of these parameters along hyporheic flow paths. 3. The chemical composition of the hyporheic pore water reflected the connectivity with the surface water, as expressed in the availability of nitrate and oxygen. Conversely, microbiological parameters in all hyporheic locations were different from the surface waters, suggesting that the microbial activity in the water changes rapidly once the water enters the hyporheic zone. This feature was prin‐ cipally manifested in higher live–dead ratios and lower leucine aminopeptidase (an activity related to nitrogen acquisition) in the hyporheic pore waters. 4. Overall, bacterial cell concentration and extracellular enzyme activities increased along hyporheic flow paths, with a congruent decrease in inorganic nutrients and dissolved organic matter quantity and apparent molecular size. 5. Our findings show two important functions of the hyporheic zone during drought: (1) deeper (−50 cm) water-saturated layers can act as a refuge for microbial activity; and (2) the hyporheic zone shows high rates of carbon and nitrogen turnover when water residence times are longer during drought. These rates might be even enhanced by an increase in living microbes in the remaining moist locations of the hyporheic zone FP7 People: Marie-Curie Actions, Grant/ Award Number: 607150; FP7 Environment, Grant/Award Number: 603629-ENV-6.2.1

Hydrological drought is a process of natural desiccation mainly due to large shortage of rainfall events. Reduced precipitations and prolonged droughts are spreading worldwide and threaten the integrity of aquatic ecosystems. Most Mediterranean streams have an intermittent flow which may become more variable and with larger duration of their no-flow periods under climate change. The enlargement of the dry period can importantly influence the ecosystem functioning, altering the microbiota inhabiting the streambed sediment as well as the processes they carry out (e.g. nutrients cycling). Consequently, hydrological alterations can reduce, limit or change microbial community functions, structure and composition, and therefore compromise the overall aquatic ecosystem functioning. The main objectives of this thesis are to study the responses of bacteria archaea and fungi inhabiting sediment to prolonged dry phase events and to wet episodes, spacing from punctual rains to rewetting events La sequía hidrológica es un proceso de desecación natural debido principalmente a la gran escasez de eventos de lluvia. Las precipitaciones reducidas y las sequías prolongadas se están extendiendo por todo el mundo y amenazan la integridad de los ecosistemas acuáticos. La mayoría de las corrientes mediterráneas tienen un flujo intermitente que puede volverse más variable y con una mayor duración de sus períodos sin flujo bajo el cambio climático. La ampliación del período seco puede influir de manera importante en el funcionamiento del ecosistema, alterando la microbiota que habita en el sedimento fluvial, así como los procesos que llevan a cabo (por ejemplo, el ciclo de nutrientes). En consecuencia, las alteraciones hidrológicas pueden reducir, limitar o cambiar las funciones, la estructura y la composición de la comunidad microbiana y, por lo tanto, comprometer el funcionamiento general del ecosistema acuático. Los objetivos principales de esta tesis son estudiar las respuestas de bacterias, arqueas y hongos que habitan en sedimentos a eventos prolongados de fase seca y episodios húmedos, espaciando desde lluvias puntuales hasta eventos de rehumectación Programa de Doctorat en Ciència i Tecnologia de l'Aigua

The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (

Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology. Made available in DSpace on 2018-11-22T00:48:49Z (GMT). No. of bitstreams: 1 2018JosiMicrobiomeDirect.pdf: 1270795 bytes, checksum: aa05ddeb2cf5aa8b11561434538baf79 (MD5) Previous issue date: 2018-11-19

Composting is the process of natural degradation of organic matter carried out by environmental microorganisms whose metabolic activities cause the mineralization and partial humification of substances in the pile. This compost can be beneficially applied to the soil as organic fertilizer in horticulture and agriculture. The number of studies involving microbial inoculants has been growing, and they aim to improve processes such as composting. However, the behavior of these inoculants and other microorganisms during the composting process have not yet been described. In this context, this work aimed to investigate the effects of using a microbial inoculum that can improve the composting process and to follow the bacterial population dynamics throughout the process using the high-resolution melt (HRM) technique. To do so, we analysed four compost piles inoculated with Bacillus cereus, Bacillus megaterium, B. cereus + B. megaterium and a control with no inoculum. The analyses were carried out using samples collected at different stages of the process (5th to 110th days). The results showed that the bacterial inocula influenced the process of composting, altering the breakdown of cellulose and hemicelluloses and causing alterations to the temperature and nitrogen levels throughout the composting process. The use of a universal primer (rDNA 16S) allowed to follow the microbial succession during the process. However, the design of a specific primer is necessary to follow the inoculum throughout the composting process with more accuracy. RESUMO A compostagem é um processo de degradação natural da matéria orgânica realizado por microrganismos presentes no ambiente, levando a mineralização e humificação parcial das substâncias presentes na pilha, esse composto formado pode ser beneficamente aplicado ao solo como fertilizante orgânico na horticultura e agricultura. O número de estudos envolvendo inoculantes microbianos é crescente, os quais tem por objetivo a otimização de processos de compostagem. Contudo, o comportamento desses inoculantes e da microbiota ao longo do processo não tem sido caracterizado. Nesse contexto, este trabalho foi realizado com o objetivo de avaliar o efeito da utilização de um inóculo bacteriano que promova melhorias no processo de compostagem, bem como o de acompanhar a dinâmica populacional bacteriana ao longo de todo o processo através da técnica de High Resolution Melt (HRM). Para isso foram analisados quatro pilhas de compostagem inoculadas com Bacillus cereus, Bacillus megaterium, B. cereus + B. megaterium e o controle sem adição de inóculo. Foram realizadas análises químicas e moleculares (HRM) das amostras coletadas em diferentes períodos da compostagem (5º ao 110º dias). Os resultados mostraram que os inóculos bacterianos influenciaram no processo de compostagem com alteração na degradação de celulose, hemicelulose bem como alteração da temperatura e níveis de nitrogênio ao longo da compostagem. A utilização de um primer universal (rDNA 16S) permitiu acompanhar a sucessão bacteriana ao longo do processo, nos tratamentos. Contudo a construção de um primer específico é necessário para acompanhar de maneira mais precisa o inóculo durante o desenvolvimento da compostagem.

Biofilm communities are exposed to long periods of desiccation in temporary streams. We investigated how water flow intermittency affected the bacterial community structure colonizing three different streambed compartments in a Mediterranean stream. Massive parallel sequencing revealed different bacterial communities in biofilms from sand sediments and cobbles. Bacterial communities were similar (62% of shared operational taxonomic units) in the epipsammic and hyporheic biofilms, and more diverse than those in the epilithic biofilms. The non-flow phase caused a decrease of bacterial diversity in the biofilms, when communities included only bacterial taxa assumed to be adapted to water stress. The most sensitive bacterial communities to flow intermittency were in the epilithic, where the exposure to physical stress was the highest. In sand sediments a wide group of bacterial taxa was tolerant to desiccation. During non-flow the proliferation of opportunistic taxa in the superficial compartments evidenced the biological link with the terrestrial environment. Bacterial communities better tolerate rewetting than desiccation, since a major number of taxa tolerant to rewetting occurred in all biofilms. Overall, bacterial communities in sandy compartments showed higher resistance to flow intermittency than those in epilithic biofilms. Droughts are severely increasing in temperate regions worldwide and are usually associated with temporal and spatial increases of non-flow periods in streams and rivers. As a result, many systems become temporary, with unknown biogeochemical and ecological consequences for biodiversity

River and stream biofilms in mediterranean fluvial ecosystems face both extreme seasonality as well as arrhythmic fluctuations. The hydrological extremes (droughts and floods) impose direct changes in water availability but also in the quantity and quality of organic matter and nutrients that sustain the microbial growth. This review analyzes how these ecological pulses might determine unique properties of biofilms developing in mediterranean streams. The paper brings together data from heterotrophic and autotrophic community structure, and extracellular enzyme activities in biofilms in mediterranean streams. Mediterranean stream biofilms show higher use of peptides during the favorable period for epilithic algae development (spring), and preferential use of cellulose and hemicellulose in autumn as a response to allochthonous input. The drying process causes the reduction in bacterial production and chlorophyll biomass, but the rapid recovery of both autotrophs and heterotrophs with rewetting indicates their adaptability to fluctuations. Bacteria surviving the drought are mainly associated with sediment and leaf litter which serve as "humid refuges". Some algae and cyanobacteria show resistant strategies to cope with the drought stress. The resistance to these fluctuations is strongly linked to the streambed characteristics (e.g., sediment grain size, organic matter accumulation, nutrient content) This study was funded by the projects CGL2011-30151-C02-01, and SCARCE (Consolider-Ingenio 2010 CSD2009-00065) of the Spanish Ministry of Economy and Competitiveness; the Italy-Spain Exchange Project CNR-CSIC 2006IT0010; and the EU project MIRAGE (FP7-ENV-2007-1 n.211732)

12 pages, 4 figures, 1 table, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2017.00636/full#supplementary-material, One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection, his study is part of the program of the Carbon Biogeochemistry in Boreal Aquatic Systems (CarBBAS) Industrial Research Chair, co-funded by the Natural Science and Engineering Research Council of Canada (NSERC) and Hydro-Quebec

Advances in genetic and immunological approaches during the last few decades have transformed medicine and biomedical research. The human genome and the genomes of numerous model organisms are now fully sequenced. Initial exploitation of this wealth of genetic information has begun to revolutionize research on these species, and the applications derived from it. Progress in understanding the ecology of microorganisms (including marine taxa) has followed closely on the heels of these advances, owing to the tremendous benefit afforded by major technological advances in biomedicine. Through the application of these novel approaches and new technologies, marine microbial ecology has moved from a minor footnote within marine biology and biological oceanography during the 1950s and ‘60s to the focus of much of our present interest in the ocean. During the intervening half-century we have learned a great deal regarding the overall abundances, distributions and activities of microorganisms in the sea. Recognition of the extraordinary diversity of marine microbes, the predominant role that they play in global biogeochemical processes, and the potential for natural or engineered microbial products to benefit humankind, has placed marine microbes in the spotlight of both scientific and popular attention. Our fascination with these minute denizens of the ocean is not likely to wane anytime soon. Recent studies have indicated that we still know relatively little about the breadth of microbial diversity in marine ecosystems. In addition, many (most?) of the predominant marine microbial forms in nature have not yet been brought into laboratory culture. Thus, our knowledge is still rudimentary with respect to the spectra of biochemical, physiological and behavioral abilities of these species, and the study of marine microbes will remain a major focus of investigations in marine science well into the foreseeable future. As a large cadre of researchers moves headlong into this work, we can expect many new discoveries and more paradigm shifts regarding the composition and function of marine microbial communities. Los avances en los campos de la genética y la inmunología durante las últimas décadas han transformado las investigaciones de medicina y biomedicina. El genoma humano y el de muchos otros organismos modelo han sido completamente secuenciados. La explotación de esta importante información genética ha empezado a revolucionar la investigación de estas especies y las aplicaciones derivadas de ésta. El progreso en el conocimiento de la ecología de los microorganismos (incluyendo los marinos) ha seguido muy de cerca los avances tecnológicos en biomedicina. La aplicación de nuevas aproximaciones y nuevas tecnologías ha permitido que la ecología microbiana haya pasado de ser una nota a pie de página a ser el tema principal en muchos de los estudios en el océano. Durante los últimos 50 años hemos aprendido aspectos acerca de las abundancias, distribuciones y actividades de los microorganismos marinos. El reconocimiento de la extraordinaria diversidad de los microbios marinos, la importancia de su papel en los ciclos biogeoquímicos y las posibles aplicaciones de los productos fabricados por los microorganismos en beneficio de la humanidad, ha colocado los microbios marinos en el punto de mira tanto de los científicos como del público en general. Nuestra fascinación por estos seres diminutos es posible que prevalezca mucho tiempo. Estudios recientes han indicado que todavía conocemos relativamente poco acerca de la gran diversidad de microorganismos en sistemas marinos. Además, muchos (la mayoría?) de las formas predominantes en la naturaleza todavía no se han logrado cultivar en el laboratorio, lo que nos indica que nuestro conocimiento es todavía rudimentario en relación con las habilidades bioquímicas, fisiológicas y de comportamiento de estos microorganismos. Así pues, previsiblemente, el estudio de los microbios ocupará una gran parte de las investigaciones en ciencias marinas en el futuro. A medida que aumenten el número de investigadores dedicados a estos estudios, se vaticina muchos descubrimientos nuevos, así como nuevos paradigmas relacionados con la composición y función de las comunidades microbianas marinas.

Conventional swine manure treatment is performed by anaerobic digestion, but nitrogen is not treated. Microbial Fuel Cells (MFCs) allow organic matter and nitrogen removal with concomitant electricity production. MFC microbiomes treating industrial wastewaters as swine manure have not been characterized. In this study, a multidisciplinary approach allowed microbiome relation with nutrient removal capacity and electricity production. Two different MFC configurations (C-1 and C-2) were used to treat swine manure. In C-1, the nitrification and denitrification processes took place in different compartments, while in C-2, simultaneous nitrification-denitrification occurred in the cathode. Clostridium disporicum and Geobacter sulfurreducens were identified in the anode compartments of both systems. C. disporicum was related to the degradation of complex organic matter compounds and G. sulfurreducens to electricity production. Different nitrifying bacteria populations were identified in both systems because of the different operational conditions. The highest microbial diversity was detected in cathode compartments of both configurations, including members of Bacteroidetes, Chloroflexiaceae and Proteobacteria. These communities allowed similar removal rates of organic matter (2.02-2.09kg CODm-3d-1) and nitrogen (0.11-0.16kgNm-3d-1) in both systems. However, they differed in the generation of electric energy (20 and 2mWm-3 in C-1 and C-2, respectively) This research was financially supported by the Company Abengoa Water within the TEcoAgua project (CEN-20091028), the Spanish Government (CTQ2011-23632) and the Catalan Government (2014 FI-B 00093 and 2012 FI-B 00941)

The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterisation of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol (MeSH) and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria, including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments, and could represent a shift from the notion that DMSP is the only significant precursor of DMS.

The aim of this study was to evaluate the diversity of rhizobial isolates obtained from root nodules of pigeonpea plants grown at the eastern edge of the Brazilian Pantanal. The bacterial isolates were isolated from root nodules from field-growing pigeonpea grown in two rural settlements of the Aquidauana municipality. The bacterial isolates were characterized phenotypically by means of cultural characterization, intrinsic antibiotic resistance (IAR), salt and high incubation temperature tolerance, and amylolytic and cellulolytic activities. The molecular characterization of the bacterial isolates was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and Box-polymerase chain reaction (PCR) techniques. In addition, the symbiotic performance of selected rhizobial isolates was evaluated in a greenhouse experiment using sterile substrate. The phenotypic characterization revealed that the bacterial strains obtained from pigeonpea root nodules presented characteristics that are uncommon among rhizobial isolates, indicating the presence of new species nodulating the pigeonpea plants in the Brazilian Pantanal. The molecular fingerprinting of these bacterial isolates also showed a highly diverse collection, with both techniques revealing less than 25% similarity among bacterial isolates. The evaluation of symbiotic performance also indicated the presence of microorganisms with high potential to increase the growth and nitrogen content at the shoots of pigeonpea plants. The results obtained in this study indicate the presence of a highly diversified rhizobial community nodulating the pigeonpea at the eastern edge of the Brazilian Pantanal.

Diazotrophic bacteria isolated from banana plants were characterized by morphological and physiological aspects. Three different groups of these plant-bacteria could be established. Two of them showed similarity to species of the Herbaspirillum genus. The third one was different because used only a few carbon substrates and produced water diffusible compounds that fluoresced under UV light. All three bacterial groups were thin rods with mono or bipolar flagella, presented negative reaction in Gram stain, showed catalase activity, were able to reduce nitrate and grew better in semi-solid JNFb medium at 31ºC. The nitrogenase activity was detected in semi-solid N-free JNFb medium and expressed higher values when pH ranged from 6.5 to 7.0 (groups I and II) and 6.0 to 6.5 (group III). The diazotrophs isolated from banana plants were distinct from species of Herbaspirillum previously identified in gramineous plants. Bactérias diazotróficas do tipo Herbaspirillum isoladas de bananeiras foram avaliadas pelas características morfológicas e fisiológicas de crescimento. Três grupos de bactérias foram estabelecidos, sendo dois relacionados às espécies de Herbaspirillum e diferentemente o terceiro grupo apresentou habilidade em crescer com poucos substratos orgânicos e produziu substância fluorescente em meio B de King. As bactérias dos três grupos eram bastonetes com flagelos mono ou bipolares, apresentaram reação negativa na coloração de Gram, expressaram atividade de catalase e oxidade, foram capazes de reduzir o nitrato e cresceram melhor em meio JNFb semi-sólido incubado a 31ºC. A atividade da nitrogenase, medida através da atividade de redução de acetileno, foi máxima em meio JNFb semi-sólido, após o ajuste de pH na faixa de 6,0 a 7,0 (grupos I e II) e 5,5 a 6,5 (grupo III). As bactérias diazotróficas associadas às bananeiras são diferentes das espécies de Herbaspirillum anteriormente identificadas em gramíneas.

Advances in genetic and immunological approaches during the last few decades have transformed medicine and biomedical research. The human genome and the genomes of numerous model organisms are now fully sequenced. Initial exploitation of this wealth of genetic information has begun to revolutionize research on these species, and the applications derived from it. Progress in understanding the ecology of microorganisms (including marine taxa) has followed closely on the heels of these advances, owing to the tremendous benefit afforded by major technological advances in biomedicine. Through the application of these novel approaches and new technologies, marine microbial ecology has moved from a minor footnote within marine biology and biological oceanography during the 1950s and ‘60s to the focus of much of our present interest in the ocean. During the intervening half-century we have learned a great deal regarding the overall abundances, distributions and activities of microorganisms in the sea. Recognition of the extraordinary diversity of marine microbes, the predominant role that they play in global biogeochemical processes, and the potential for natural or engineered microbial products to benefit humankind, has placed marine microbes in the spotlight of both scientific and popular attention. Our fascination with these minute denizens of the ocean is not likely to wane anytime soon. Recent studies have indicated that we still know relatively little about the breadth of microbial diversity in marine ecosystems. In addition, many (most?) of the predominant marine microbial forms in nature have not yet been brought into laboratory culture. Thus, our knowledge is still rudimentary with respect to the spectra of biochemical, physiological and behavioral abilities of these species, and the study of marine microbes will remain a major focus of investigations in marine science well into the foreseeable future. As a large cadre of researchers moves headlong into this work, we can expect many new discoveries and more paradigm shifts regarding the composition and function of marine microbial communities., Los avances en los campos de la genética y la inmunología durante las últimas décadas han transformado las investigaciones de medicina y biomedicina. El genoma humano y el de muchos otros organismos modelo han sido completamente secuenciados. La explotación de esta importante información genética ha empezado a revolucionar la investigación de estas especies y las aplicaciones derivadas de ésta. El progreso en el conocimiento de la ecología de los microorganismos (incluyendo los marinos) ha seguido muy de cerca los avances tecnológicos en biomedicina. La aplicación de nuevas aproximaciones y nuevas tecnologías ha permitido que la ecología microbiana haya pasado de ser una nota a pie de página a ser el tema principal en muchos de los estudios en el océano. Durante los últimos 50 años hemos aprendido aspectos acerca de las abundancias, distribuciones y actividades de los microorganismos marinos. El reconocimiento de la extraordinaria diversidad de los microbios marinos, la importancia de su papel en los ciclos biogeoquímicos y las posibles aplicaciones de los productos fabricados por los microorganismos en beneficio de la humanidad, ha colocado los microbios marinos en el punto de mira tanto de los científicos como del público en general. Nuestra fascinación por estos seres diminutos es posible que prevalezca mucho tiempo. Estudios recientes han indicado que todavía conocemos relativamente poco acerca de la gran diversidad de microorganismos en sistemas marinos. Además, muchos (la mayoría?) de las formas predominantes en la naturaleza todavía no se han logrado cultivar en el laboratorio, lo que nos indica que nuestro conocimiento es todavía rudimentario en relación con las habilidades bioquímicas, fisiológicas y de comportamiento de estos microorganismos. Así pues, previsiblemente, el estudio de los microbios ocupará una gran parte de las investigaciones en ciencias marinas en el futuro. A medida que aumenten el número de investigadores dedicados a estos estudios, se vaticina muchos descubrimientos nuevos, así como nuevos paradigmas relacionados con la composición y función de las comunidades microbianas marinas.

Este trabalho objetivou selecionar bactérias diazotróficas isoladas de bananeira (Musa spp.) e avaliar sua influência no crescimento de mudas micropropagadas. Bactérias do tipo Herbaspirillum e relacionadas a Burkholderia cepacia foram inoculadas em plântulas de banana cv. Prata Anã e cv. Caipira. As bananeiras cv. Prata Anã, cultivadas in vitro com substrato pobre em N, apresentaram maior crescimento na presença de bactérias do tipo Herbaspirillum, ao passo que as bananeiras cv. Caipira cresceram melhor com o inóculo contendo bactérias do gênero Burkholderia. Em casa de vegetação, as bananeiras cv. Caipira crescidas em sacolas de plástico contendo areia e vermiculita (1:2), suplementada com a solução de Hoagland contendo 5 mg L-1 de N, apresentaram maior crescimento quando da inoculação simultânea dos dois gêneros de bactérias, em comparação à inoculação individual. A inoculação simultânea proporcionou um crescimento nas bananeiras equivalente ao observado nas plantas-controles adubadas com 50 mg L-1 de N no substrato, porém o teor e o acúmulo de N na parte aérea das bananeiras foram menores. A contribuição de bactérias diazotróficas no crescimento de bananeiras é demonstrada pela primeira vez. The objective of this work was to select strains of diazotrophic bacteria associated with banana plants and to determine micropropagated plantlet-growth-promotion by their inoculation with diazotrophs. Isolates of Herbaspirillum-like and Burkholderia cepacia related bacteria were inoculated in plantlets of banana cv. Prata Anã and the cultivar Caipira. Plantlets of banana cv. Prata Anã grown in vitro on a poor nitrogen substrate presented higher fresh weight when Herbaspirillum-like bacteria were used as inoculum, while the banana cv. Caipira grew better with the inoculation of Burkholderia cepacia related bacteria. Nevertheless, plants of the cultivar Caipira cultivated in plastic bags filled with sand and vermiculite (1:2) and supplied with Hoagland's solution containing 5 mg L-1 of N grew faster with the inoculation of Herbaspirillum-like and Burkholderia cepacia related bacteria. This effect was similar to 50 mg L-1 of N fertilizer added to the positive control. However, the control plants showed higher N content in their shoots when compared to bacterial inoculated plants. This work constitutes the first announcement of banana plant-growth-promotion by diazotrophic bacteria.

A mutant strain of Rhodobacter sphaeroides, altered in carotenoid biosynthesis. was compared to the wild type in relation to the physiological response of both strains to different light intensities (230-925 lux). Absorption spectra analysis showed that spheroidene, the main carotenoid present in this species, was substituted by chloroxanthin (hydroxyneurosporene) in the mutant strain. The mutation does not affect significantly the growh of the mutant under neither photoorganoheterotrophic nor chemoorganoheterotrophic metabolisms. Mutant cells growing anaerobically at light intensities below 800 lux, surprisingly showed higher growth rates than wild type cells. At light intensities above 800 lux, growth rates of both strains were very similar. Growth rates in chemoorganotrophic metabolism were much higher than in photoorganotrophic growth for both strains. Although pigments do not intervene in nonphotosynthetic metabolism, the wild type strain showed a higher growth rate than the mutant strain. In addition to growth rate measurement, pigment content was studied in order to characterize the physiological behaviour of the mutant. In the wild type strain, specific pigment content decreased as light intensity increased. Bacteriochlorophyll and carotenoids showed the same response. On the contrary, for the mutant cells, bacteriochlorophyll specific content was much higher at high light intensities than at the lower ones. Carotenoids had very low specific content. which was independent of light intensity. Both the physiological implications and the possible ecological meaning of that behaviour are discussed.

The association of wild grasses with diazotrophic bacteria in Brazilian biomes is poorly understood. The isolation and characterization of bacteria associated with wild grasses can contribute to understand the diazotrophic ecology as well as to identify bacteria with biotechnological applications. In this study, we isolated and characterized diazotrophic bacterial isolates from Oryza glumaepatula collected in Cerrado and Forest areas of the Amazon in Roraima State, Brazil. Healthy O. glumepatula plants were collected at five sampling sites at Forest and seven at Cerrado, respectively. The plants were collected at the Cerrado areas in September 2008 while the Forest plants were collected in June/2008 and April/2009. The plants and the soil adhering to the roots were transferred to pots and grown for 35 days in greenhouse conditions. During the harvest, the shoots and the roots were crushed separately in a saline solution; the suspension was diluted serially and inoculated in Petri dishes containing Dyg’s medium. All distinct bacterial colonies were purified in the same medium. The diazotrophic capacity of each bacterium in microaerophilic conditions was assessed in semisolid BMGM medium. In addition, the pellicles forming bacterial isolates were also evaluated by PCR amplification for nifH gene. The diversity of nifH+ bacteria was analyzed by Box-PCR fingerprinting. For selected strains, the growth promoting capacity of O. sativa as a model plant was also evaluated. A total of 992 bacterial isolates were obtained. Fifty- one bacteria were able to form pellicles in the semisolid medium and 38 also positively amplified the 360bp nifH gene fragment. Among the 38 nifH+ isolates, 24 were obtained from the shoots, while 14 originated from the roots. The Box-PCR profiles showed that the bacterial isolates obtained in this study presented a low similarity with the reference strains belonging to the Herbaspirillum, Azospirillum and Burkholderia genus. The growth- promoting ability was confirmed for at least five isolates. For these bacteria, the root and shoot growing results showed higher increases when compared to those observed in plants inoculated with the evaluated reference strains. These results indicate that O. glumaepatula is colonized by a high diverse diazotrophic community in the Brazilian Amazon. Further investigations are now being carried out to determine the taxonomic positions of these isolates and their growth promoting mechanisms. La asociación de gramíneas silvestres con bacterias diazotróficas en los biomas brasileños es poco conocida. El aislamiento y caracterización de las bacterias asociadas con gramíneas silvestres puede contribuir a entender la ecología de las diazotróficas y bacterias con aplicaciones biotecnológicas. En este estudio, caracterizamos aislamientos bacterianos de diazotróficas de Oryza glumaepatula recolectadas en Cerrado y zonas boscosas de la Amazonía en el estado de Roraima, Brasil. Plantas sanas de O. glumepatula fueron recolectadas en cinco zonas boscosas y siete en Cerrado. Las plantas de Cerrado fueron recolectadas en septiembre 2008, mientras que las del bosque en Junio 2008 y Abril 2009. Las plantas y el suelo adherido a las raíces se transfirieron a macetas y se cultivaron durante 35 días en condiciones de invernadero. Durante la cosecha, los brotes y las raíces se trituraron por separado en una solución salina, la suspensión se diluyó en serie y se inocularon en placas Petri que contenían medio Dyg. Todas las colonias de bacterias se purificaron en el mismo medio. Se evaluó la capacidad diazotrófica de cada bacteria en condiciones microaerofílicas en medio semisólido BMGM. Además, los aislamientos bacterianos que formaron películas se evaluaron también mediante amplificación por PCR para el gen nifH. La diversidad de bacterias nifH+ se analizó por Huella Genética utilizando la Reacción en Cadena de la Polimerasa. Para las cepas seleccionadas, la capacidad de promover el crecimiento de O. sativa como modelo de planta también se evaluó. Se obtuvo un total de 992 cepas bacterianas. Cincuenta y un bacterias fueron capaces de formar películas en el medio semisólido y 38 amplificaron positivamente el fragmento 360bp del gen nifH. De los 38 aislamientos de nifH+, 24 fueron obtenidos de los brotes, mientras que 14 se originaron a partir de las raíces. Los perfiles de PCR-Box mostraron que los aislamientos bacterianos obtenidos en este estudio presentaron una baja similitud con las cepas de referencia pertenecientes a Herbaspirillum, Azospirillum y el género Burkholderia. La capacidad promotora del crecimiento fue confirmada por al menos cinco aislamientos. Para esta bacteria, la raíz y brote mostraron resultados de crecimiento mayores en comparación con los observados en las plantas inoculadas con las cepas de referencia. Estos resultados indican que O. glumaepatula es colonizada por una muy diversa comunidad diazotrófica en la Amazonia brasileña. Se están llevando a cabo otras investigaciones para esclarecer la taxonomía de estas cepas y sus mecanismos para promover el crecimiento.

Living organisms constantly interact with their habitats, selectively taking up compounds from their surroundings to meet their particular needs but also excreting metabolic products and thus modifying their environment. The small size, ubiquity, metabolic versatility, flexibility, and genetic plasticity (horizontal transfer) of microbes allow them to tolerate and quickly adapt to unfavorable and/or changing environmental conditions. The consumption of resources and the formation of metabolic products by spatially separated microbial populations constitute the driving forces that lead to chemical gradient formation. Communication and cooperation, both within and among bacterial species, have produced the properties that give these organisms a selective advantage. Observations of a wide range of natural habitats have established that bacteria do not function as individuals; rather, the vast majority of bacteria in natural and pathogenic ecosystems live in biofilms, defined as surface-associated, complex aggregates of bacterial communities that are attached to solid substrates and embedded in a polymer matrix of their own production. The spatial configurations of biofilms reach levels of complexity nearing those of multicellular eukaryotes. Microbial consortia have played important roles throughout the history of life on Earth, from the microbial mats (a type of biofilm) that were probably the first ecosystems in the early Archean, to the complex microbiota of the intestinal tract of different animals.

Water flowing through hyporheic river sediments or artificial recharge facilities promotes the development of microbial communities with sediment depth. We performed an 83-day mesocosm infiltration experiment, to study how microbial functions (e.g., extracellular enzyme activities and carbon substrate utilization) are affected by sediment depth (up to 50. cm) and different oxygen concentrations. Results indicated that surface sediment layers were mainly colonized by microorganisms capable of using a wide range of substrates (although they preferred to degrade carbon polymeric compounds, as indicated by the higher β-glucosidase activity). In contrast, at a depth of 50. cm, the microbial community became specialized in using fewer carbon substrates, showing decreased functional richness and diversity. At this depth, microorganisms picked nitrogenous compounds, including amino acids and carboxyl acids. After the 83-day experiment, the sediment at the bottom of the tank became anoxic, inhibiting phosphatase activity. Coexistence of aerobic and anaerobic communities, promoted by greater physicochemical heterogeneity, was also observed in deeper sediments. The presence of specific metabolic fingerprints under oxic and anoxic conditions indicated that the microbial community was adapted to use organic matter under different oxygen conditions. Overall the heterogeneity of oxygen concentrations with depth and in time would influence organic matter metabolism in the sediment tank This work has been performed in the framework of project SCARCE Consolider-Ingenio 2010 program (reference CSD2009-00065). A. F. benefited from a grant (FI-DGR 2013) from the Catalan Government. X. S. acknowledges support from ICREA Academia. D. F-G acknowledges the financial support provided by the Spanish Ministry of Science through project FEAR (CGL2012-38120). AM R. acknowledges the financial support provided by the Spanish Ministry of Economy and Competitiveness through project FLUMED-HOTSPOTS (CGL2011-30151-C02). SR acknowledges the support of the Provincia Autonoma di Trento and the European Commission. This project has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no PCOFUND-GA-2008-226070. We also thank anonymous reviewers for their suggestions