Inferring causal relations from observational long-term carbon and water fluxes records.

Land, atmosphere and climate interact constantly and at different spatial and temporal scales. In this paper we rely on causal discovery methods to infer spatial patterns of causal relations between several key variables of the carbon and water cycles: gross primary productivity, latent heat energy flux for evaporation, surface air temperature, precipitation, soil moisture and radiation. We introduce a methodology based on the convergent cross-mapping (CCM) technique. Despite its good performance in general, CCM is sensitive to (even moderate) noise levels and hyper-parameter selection. We present a robust CCM (RCCM) that relies on temporal bootstrapping decision scores and the derivation of more stringent cross-map skill scores. The RCCM method is combined with the information-geometric causal inference (IGCI) method to address the problem of strong and instantaneous variable coupling, another important and long-standing issue of CCM. The proposed methodology allows to derive spatially explicit global maps of causal relations between the involved variables and retrieve the underlying complexity of the interactions. Results are generally consistent with reported patterns and process understanding, and constitute a new way to quantify and understand carbon and water fluxes interactions.

Dark fermentation: isolation and characterization of hydrogen-producing strains from sludges.

To improve bacterial hydrogen production, ten hydrogen-producing strains belonging to Clostridium spp. were isolated from various sludges under low vacuum. Hydrogenogenesis by dark fermentation in batch cultures of these strains was optimal at about 35 degrees C and an initial pH of 6.5, which for all strains gradually dropped to ca. pH 4 during the fermentation. Clostridium roseum H5 and C. diolis RT2 had the highest hydrogen yields per total substrate (120 ml H2/g initial COD). Substrate consumption alone by C. beijerinckii UAM and C. diolis RT2 reached 573 and 475 ml H2/g consumed COD, respectively. Butyric acid fermentation was predominant, with butyrate and acetate as the major by-products and propionate, ethanol, and lactate as secondary metabolites. The acetate:butyrate ratios and fermentation pathways varied depending on the strains and environmental conditions. Hydrogenogenesis was studied in greater detail in C. saccharobutylicum H1. In butyric acid fermentation by this representative strain, acetoacetate was detected as an intermediate metabolite. Hydrogenogenesis was also analyzed in an enrichment culture, which behaved similarly to the axenic cultures.

Dark fermentation: isolation and characterization of hydrogen-producing strains from sludges

To improve bacterial hydrogen production, ten hydrogen-producing strains belonging to Clostridium spp. were isolated from various sludges under low vacuum. Hydrogenogenesis by dark fermentation in batch cultures of these strains was optimal at about 35 ºC and an initial pH of 6.5, which for all strains gradually dropped to ca. pH 4 during the fermentation. Clostridium roseum H5 and C. diolis RT2 had the highest hydrogen yields per total substrate (120 ml H2/g initial COD). Substrate consumption alone by C. beijerinckii UAM and C. diolis RT2 reached 573 and 475 ml H2/g consumed COD, respectively. Butyric acid fermentation was predominant, with butyrate and acetate as the major by-products and propionate, ethanol, and lactate as secondary metabolites. The acetate: butyrate ratios and fermentation pathways varied depending on the strains and environmental conditions. Hydrogenogenesis was studied in greater detail in C. saccharobutylicum H1. In butyric acid fermentation by this representative strain, acetoacetate was detected as an intermediate metabolite. Hydrogenogenesis was also analyzed in an enrichment culture, which behaved similarly to the axenic cultures (AU)

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Microbial consortia for hydrogen production enhancement.

Ten efficient hydrogen-producing strains affiliated to the Clostridium genus were used to develop consortia for hydrogen production. In order to determine their saccharolytic and proteolytic activities, glucose and meat extract were tested as fermentation substrates, and the best hydrogen-producing strains were selected. The C. roseum H5 (glucose-consuming) and C. butyricum R4 (protein-degrading) co-culture was the best hydrogen-producing co-culture. The end-fermentation products for the axenic cultures and co-cultures were analyzed. In all cases, organic acids, mainly butyrate and acetate, were produced lowering the pH and thus inhibiting further hydrogen production. In order to replace the need for reducing agents for the anaerobic growth of clostridia, a microbial consortium including Clostridium spp. and an oxygen-consuming microorganism able to form dense granules (Streptomyces sp.) was created. Increased yields of hydrogen were achieved. The effect of adding a butyrate-degrading bacteria and an acetate-consuming archaea to the consortia was also studied.

Methanogenesis in the sediments of Rio Tinto, an extreme acidic river.

Río Tinto (Iberian Pyritic Belt, SW Spain) is well known for its low pH (mean pH 2.3), high redox potential (> +400 mV) and high concentration of heavy metals. In this work we describe and analyse the presence of methanogenic archaea in the extreme acidic and oxidizing environment of the Tinto basin. Methane formation was measured in microcosms inoculated with sediments from the Rio Tinto basin. Methanol, formate, volatile fatty acids and lactate stimulated the production of methane. Methane formation was associated with a decrease of redox potential and an increase in pH. Cores showed characteristic well-defined black bands in which a high acetate concentration was measured among the otherwise reddish-brown sediments with low acetate concentration. Methanosaeta concilii was detected in the black bands. In enrichment cultures, M. concilii (enriched with a complex substrate mixture), Methanobacterium bryantii (enriched with H(2)) and Methanosarcina barkeri (enriched with methanol) were identified. Our results suggest that methanogens thrive in micro-niches with mildly acidic and reducing conditions within Rio Tinto sediments, which are, in contrast, immersed in an otherwise extremely acidic and oxidizing environment.

Analysis of microbial community during biofilm development in an anaerobic wastewater treatment reactor.

The formation, structure, and biodiversity of a multispecies anaerobic biofilm inside an Upflow Anaerobic Sludge Bed (UASB) reactor fed with brewery wastewater was examined using complementary microbial ecology methods such us fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), and cloning. The biofilm development can be roughly divided into three stages: an initial attachment phase (0-36 h) characterized by random adhesion of the cells to the surface; a consolidation phase (from 36 h to 2 weeks) defined by the appearance of microcolonies; and maturation phase (from 2 weeks to 2 months). During the consolidation period, proteobacteria with broad metabolic capabilities, mainly represented by members of alpha-Proteobacteria class (Oleomonas, Azospirillum), predominated. Beta-, gamma-, delta- (both syntrophobacteria and sulfate-reducing bacteria) and epsilon- (Arcobacter sp.) Proteobacteria were also noticeable. Archaea first appeared during the consolidation period. A Methanospirillum-like methanogen was detected after 36 h, and this was followed by the detection of Methanosarcina, after 4 days of biofilm development. The mature biofilm displayed a hill and valley topography with cells embedded in a matrix of exopolymers where the spatial distribution of the microorganisms became well-established. Compared to the earlier phases, the biodiversity had greatly increased. Although alpha-Proteobacteria remained as predominant, members of the phyla Firmicutes, Bacteroidete, and Thermotogae were also detected. Within the domain Archaea, the acetoclastic methanogen Methanosaeta concilii become dominant. This study provides insights on the trophic web and the shifts in population during biofilm development in an UASB reactor.

Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater.

Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH), and scanning and transmission electron microscopy. We propose here that the different types of granules reflect the different stages in the life cycle of granules. Young granules were small, black, and compact and harbored active cells. Gray granules were the most abundant granules. These granules have a multilayer structure with channels and void areas. The core was composed of dead or starving cells with low activity. The brown granules, which were the largest granules, showed a loose and amorphous structure with big channels that resulted in fractured zones and corresponded to the older granules. Firmicutes (as determined by FISH) and Nitrospira and Deferribacteres (as determined by cloning and sequencing) were the predominant Bacteria. Remarkably, Firmicutes could not be detected in the brown granules. The methanogenic Archaea identified were Methanosaeta concilii (70 to 90% by FISH and cloning), Methanosarcina mazei, and Methanospirillum spp. The phenotypic appearance of the granules reflected the physiological condition of the granules. This may be valuable to easily select appropriate seed sludges to start up other reactors.