Characterization of a sulfide-oxidizing biofilm developed in a packed-column reactor

The potential of microbial mats to develop sulfide-oxidizing biofims was explored. A bioreactor specially designed for the treatment of sulfide-containing effluents was inoculated with a microbial-mat sample, and a complex microbial biofilm with sulfide-oxidation activity developed. The microbial composition of the biofilm was studied by pigment, microscopy, and 16S rRNA gene analyses. Purple sulfur bacteria and diatoms were observed by microscopy, chlorophyll a and bacteriochlorophyll a were detected in the pigment analysis, and high genetic diversity was found in the 16S rRNA gene library. Specialized anaerobic sulfur oxidizers (i.e., phototrophic purple and green sulfur bacteria) dominated the library. Aerobic phototrophs (diatoms) also developed and the oxygen produced allowed the growth of aerobic sulfide oxidizers, such as Thiomicrospira-like spp. Cyanobacteria, which are significant organisms in natural microbial mats, did not develop in the reactor but unexpected uncultured members from the Epsilonproteobacteria developed profusely. Moreover, a variety of more minor organisms, such as members of the Cytophaga-Flavobacterium-Bacteroides (CFB) and purple non-sulfur bacteria (Roseospirillum sp.), were also present. The results showed that a complex community with high genetic and metabolic diversity, including many uncultured organisms, can develop in a laboratory-scale reactor. [Int Microbiol 2007; 10(1):29-37

Long-term patterns of an interconnected core marine microbiota

Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth’s primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade.Versión del edito

Towards a Global Perspective of the Marine Microbiome

Marine microbes play fundamental roles in nutrient cycling and climate regulation at a planetary scale. The field of marine microbial ecology has experienced major breakthroughs following the application of high-throughput sequencing and cultureindependent methodologies that have pushed the exploration of the marine microbiome to an unprecedented scale. This chapter overviews how the advances in gene- and genome-centric approaches as well as in culturing and single cell physiological methodologies in conjunction with global oceanographic circumnavigation expeditions and long-term time series are fueling our understanding of the biogeography, temporal dynamics, functional diversity, and evolutionary processes of microbial populations. We discuss how the joint effort of all those integrative approaches will help to boost our knowledge of the marine microbiome to reach a predictive understanding of how it is going to evolve in future scenarios.Versión del edito

Development and characterization of sulfide-oxidizing biofilms

Consultable des del TDXTítol obtingut de la portada digitalitzadaEn el present treball s'han desenvolupat i caracteritzat biofilms per a la detoxificació d'efluents contaminats amb compostos reduïts de sofre. En primer lloc es va dissenyar un bioreactor basat en una columna il·luminada que aporta una gran i heterogènia superfície d'adhesió per als microorganismes, i en el qual no hi ha aportació externa d'oxigen. El sistema de control, basat en el potencial redox, permet mantenir constant la concentració residual de sulfur d'hidrogen en el rang micromolar, evitant la inhibició dels microorganismes i mantenint al mateix temps la qualitat de l'efluent generat. S'han realitzat tres experiments per tal de provar el sistema, el primer amb un cultiu pur de Chlorobium limicola, i després amb mostres naturals (sediment lacustre i tapet microbià) per tal d'aconseguir biofilms complexos. Els biofilms es desenvolupen ràpidament assolint-se una elevada biomassa en tots els casos. El comportament dinàmic del sistema és més lent que el dels sistemes de biomassa en suspensió, però alhora més estable a les pertorbacions. De fet, el sistema és capaç de mantenir l'oxidació de sulfurs i la qualitat de l'efluent generat fins i tot quan les condicions de llum incident o de concentració de sulfur d'hidrogen a l'entrada del sistema canvien. S'han caracteritzat els biofilms complexos amb eines clàssiques (microscopi i anàlisi de pigments) i també amb eines moleculars (biblioteques genètiques). En primer lloc, s'han avaluat diferents mètodes d'extracció d'ADN per tal de trobar el millor per a les nostres mostres. S'ha comparat l'eficiència d'extracció quantificant l'ADN obtingut, i la diversitat recuperada en cada mètode amb electroforesi en gels de gradient desnaturalitzant (DGGE). El mètode basat en un trencament mecànic amb microesferes de vidre seguit d'una lisi enzimàtica i una extracció amb fenol és el més apropiat per a l'extracció d'aquests biofilms. La caracterització del biofilms ha revelat una elevada diversitat microbiana tant a nivell filogenètic com fisiològic. Ambdós biofilms presenten una gran riquesa d'espècies així com un elevat grau de microdiversitat entre alguns grups. S'observen algunes diferències en els grups filogenètics predominants entre els dos biofilms. S'han recuperat membres relacionats amb les subclasses Alpha i Gamma del grup Proteobacteria, amb el grup Cytophaga-Flavobacterium-Bacteroides així com amb cloroplasts d'algues en ambdós biblioteques genètiques. A més, en el biofilm desenvolupat a partir del sediment lacustre, també s'han trobat membres de les subclasses Beta i Delta-Proteobacteria, del grup Cianobacteria i dels bacteris Gram-positius de baix contingut en G+C (Firmicutes). Per contra, la biblioteca realitzada amb el biofilm desenvolupat a partir del tapet microbià conté una elevada proporció de clons relacionats amb les Epsilon-Proteobacteria i amb els Chlorobi. Tot i que els membres trobats pertanyent a tots aquests grups filogenètics són diferents, representen els mateixos grups funcionals. El sulfhídric era oxidat anaeròbicament pels bacteris fototròfics del sofre i els bacteris vermells no del sofre, i aeròbicament pels bacteris quimiolititròfics del sofre utilitzant l'oxigen produït pels organismes fototròfics oxigènics. Altres microorganismes com els bacteris heterotròfics podrien contribuir al funcionament del sistema a través del reciclatge de la matèria orgànica. En conclusió, trobem una elevada diversitat tant a nivell funcional com taxonòmic en els biofilms desenvolupats. Diferents grups funcionals representats per diferent espècies (heterotròfiques, fotoautotròfiques i quimioautotròfiques) coexisteixen al sistema. A més, també trobem microdiversitat (similitud per sobre del nivell d'espècie en la seqüència del gen 16S ADNr). Aquesta elevada diversitat podria ser molt important per al funcionament a llarg termini del reactor.This works deals with the development and characterization of complex sulfide-oxidizing biofilms. A bioreactor for biofilm development has been designed. The system is based on a non-aerated illuminated packed-column, which provides a large surface for microbial attachment. The reactor operates as a sulfidostat and the control system allows to maintain a constant concentration of residual sulfide in the micromolar range thus avoiding inhibition of sulfide oxidizers due to excessive sulfide load and ensuring a constant quality in the effluent. The system was first tested with a pure culture of Chlorobium limicola and, later on, with natural samples (freshwater lake sediment and a microbial mat) in order to develop complex biofilms. Biofilms developed vigorously on the column surface and high biomass was achieved in all the experiments. The dynamic behavior of the system was slower than in stirred reactors but more stable in front of sudden environmental changes. The system was able to process highly polluted effluents and to maintain the quality of the output generated even when conditions of light irradiance and sulfide income were suddenly changed. The biofilms developed were characterized using both, traditional techniques (i.e. microscopy and pigment analysis) and a molecular approach, in particular cloning and sequencing. First, of all, several DNA extraction procedures were evaluated in order to select the most suitable method for performing the diversity analysis of our biofilms. We compared the extraction efficiency (i.e. amount of DNA recovered), as well as the genetic diversity recovered by denaturing gradient gel electrophoresis (DGGE). A DNA extraction based on a mechanical step of bead-beating followed by enzymatic lysis and by phenol-chloroform extraction, was the most appropriate protocol for these biofilms. Microbial characterization revealed that, in both cases, highly diverse biofilms covering a wide range of phylogenetic and physiologic groups had developed. Both biofilms presented high species richness and a high degree of microdiversity within some species. Some differences were observed in the predominant phylogenetic groups present in each biofilm. We recovered members affiliated to the Alpha and Gamma subclass of the Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides group as well as plastids signatures from green algae in both biofilm libraries. Moreover, in the biofilm developed from the freshwater sample, other clones belonged to the Beta- and Delta-Proteobacteria, the Cyanobacteria and the low G+C Gram-positive whereas we recovered clones belonging to the Epsilon-Proteobacteria and to the Chlorobi only from the marine biofilm. Although members belonging to these phylogenetic groups were different in each case, they represented the same functional groups. Sulfide was oxidized both anaerobically by phototrophic sulfur bacteria and by purple nonsulfur bacteria, and aerobically by colorless sulfur bacteria using the oxygen produced by oxygenic phototrophs, as the system was non-aerated. Other groups, such heterotrophic bacteria, can also contribute to the functioning of the system by recycling organic matter. In conclusion, we found high diversity at both functional and taxonomic level. Different functional groups represented by different species (heterotrophic, photoautotrophic and chemoautotrophic microorganisms) coexisted in the bioreactor. Moreover, some of the species also showed microdiversity (similarity in 16S rDNA sequences below the species level). Such attributes could be very important for the long-term functioning and versatility of the reactor

Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans

The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.Versión del edito

Genetic and phenotypic diversity characterization of natural populations of the parasitoid Parvilucifera sinerae

Parasites exert important top-down control of their host populations. The host−parasite system formed by Alexandrium minutum (Dinophyceae) and Parvilucifera sinerae (Perkinsozoa) offers an opportunity to advance our knowledge of parasitism in planktonic communities. In this study, DNA extracted from 73 clonal strains of P. sinerae, from 10 different locations along the Atlantic and Mediterranean coasts, was used to genetically characterize this parasitoid at the species level. All strains showed identical sequences of the small and large subunits and internal transcribed spacer of the ribosomal RNA, as well as of the β-tubulin genes. However, the phenotypical characterization showed variability in terms of host invasion, zoospore success, maturation time, half-maximal infection, and infection rate. This characterization grouped the strains within 3 phenotypic types distinguished by virulence traits. A particular virulence pattern could not be ascribed to host-cell bloom appearance or to the location or year of parasite-strain isolation; rather, some parasitoid strains from the same bloom significantly differed in their virulence traits. Identical markers such as ITS and β-tubulin genes of P. sinerae strains from different geographic areas and from different years precludes their use in assessing intra-specific diversity and could indicate a recent dispersion of this species.Versión del editor2,393