Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment.

Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.

Phytoplankton composition and abundance as indicators of aquaculture effluents impact in coastal environments of mid Gulf of California.

Composition and abundance of phytoplankton in two areas of Gulf of California, one near (ND) and one far (FD) from shrimp farms discharge, were studied in 3 seasons: late fall (farms finishing operations); spring (farms not operating); and summer (farms operating). In ND, 61 diatoms, 33 dinoflagellates, 4 cyanobacteria, and 2 silicoflagellates were identified; in FD, 72 diatoms, 38 dinoflagellates, 5 cyanobacteria, and 4 silicoflagellates were found. Thirty-three species were recorded only in ND (20 diatoms, 11 dinoflagellates, 1 silicoflagellate), whereas 39 species appeared exclusively in the FD (28 diatoms, 9 dinoflagellates, 1 cyanobacteria, 1 silicoflagellate). Thirty-seven species were common for both areas (23 diatoms, 10 dinoflagellates, 3 cyanobacteria and 1 silicoflagellate). In ND, 9 species potentially toxic (3 diatoms, 5 dinoflagellates, 1 cyanobacteria) were identified. From FD, 3 species potentially toxic (2 diatoms and 1 cyanobacteria) were found. Total abundance of phytoplankton was more than double in ND than in FD. The species richness and diversity, were greater in FD. Higher phytoplankton abundance was observed when farms were operating or finishing operations. The composition and abundance of phytoplankton is a good indicator of shrimp effluents impact, diminishing the species richness and diversity, but augmenting the abundance.

Biofilm-forming capacity of two benthic microalgae, Navicula incerta and Navicula sp., on three substrates (Naviculales: Naviculaceae)

Benthic microalgae have the natural capacity to adhere to a diversity of fixed submerged substrates to form biofilms, which have important roles not only in natural ecosystems, but also in aquaculture systems. An experimental investigation was performed to assess the biofilm-forming capacity of two microalgae (Navicula incerta and Navicula sp.) on three different substrates (plastic net, fabric, and wood) under controlled temperature and light conditions. The substrates were arranged on curtains suspended from a wood stick, into plastic aquariums (45 L in capacity) filled with filtered marine water enriched with F/2 medium. The trial was carried out until the exponential growing phase of the microalgae was reached. After that, the incorporated biomass was gravimetrically calculated, and its biochemical composition was determined by standard methods. The greatest amount of incorporated dry matter was observed for Navicula sp. on fabric and the lowest was observed for wood. The highest number of cells associated with the biofilm was obtained for Navicula sp. on the plastic net (1.24 x 109 cells/m2), while the lowest was recorded for Navicula sp. on the wood (1.43 x 108 cells/m2). Significant differences in organic matter were found among the substrates, with the highest values for N. incerta on the fabric (3.22 g/m2) and the lowest for Navicula sp. on the wood (0.02 g/m2). The best biochemical profiles among the formed biofilms were observed for N. incerta on the plastic net and Navicula sp. on the fabric. The plastic net was considered the best substrate because of the stability of the biofilm and the easiness of harvesting the biomass.

Las microalgas bentónicas tienen la capacidad natural de adherirse a diversos sustratos fijos sumergidos para formar biopelículas, las cuales tienen roles importantes no solo en ecosistemas naturales sino también en sistemas de producción acuícolas. Se llevó a cabo una investigación experimental para evaluar la capacidad formadora de biopelículas de dos microalgas bentónicas (Navicula incerta y Navicula sp.) en tres diferentes sustratos (malla plástica, tela y madera), bajo condiciones controladas de temperatura y luz. Los sustratos fueron arreglados a manera de cortinas suspendidas de un tubo de PVC dentro de acuarios de plástico (45 L de capacidad) con agua marina enriquecida con el medio F/2. El experimento se llevó hasta que la fase de crecimiento exponencial de la microalga fue alcanzada. Posteriormente la biomasa incorporada fue calculada gravimétricamente, y su composición bioquímica fue determinada por métodos estándar. La mayor cantidad de materia seca se observó para N. incerta en el sustrato de tela y la menor se encontró en el de madera. El mayor número de células asociadas a la biopelícula fue registrado para Navicula sp. en malla plástica (1.24 x 109 cel/m2), mientras que el menor se encontró para Navicula sp. en madera (1.43 x 108 cels/m2). Diferencias significativas en cuanto a materia orgánica se encontraron entre los sustratos y las especies, con valores más altos para N. incerta en tela (3.22 g/m2) y más bajos para Navicula sp. en madera (0.02 ± 0.05 g/m2). Los mejores perfiles bioquímicos para las biopelículas correspondieron a las formadas por N. incerta sobre malla plástica y Navicula sp. sobre tela. La red de plástico se consideró el mejor sustrato debido a la estabilidad de la biopelícula y la facilidad para cosechar la biomasa.

Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences.

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.

Proteomic profiling of integral membrane proteins associated to pathogenicity in Vibrio parahaemolyticus strains.

Vibrio parahaemolyticus has been recognized as the causal agent of early mortality syndrome and is currently considered an emerging shrimp disease causing losses of millions in the aquaculture industry. Integral membrane proteins are widely recognized as pathogenicity factors involved in essential mechanisms for V. parahaemolyticus infection, which makes them attractive as therapeutic targets. However, their physico-chemical properties and weak expression has resulted in under-representation of these proteins in conventional bottom-up proteomics, making integral membrane proteomics a challenging task. Integral membrane proteins from a bacterial strain isolated from the hepatopancreases of white shrimp with early mortality syndrome and identified by 16S rRNA sequencing as V. parahaemolyticus and an ATCC strain that is pathogenic for humans were obtained by a sequential extraction method and subjected to relative quantification and identification by isobaric Tags for Relative and Absolute Quantitation. A homology database search resulted in identification of more than two hundred proteins, 35 of which are recognized as pathogenic factors showed statistically significant differential accumulation between the strains. These proteins are mainly associated with adherence, secretion systems, cell division, transport, lysogenization, movement and virulence. Identification of pathogenicity-related proteins in V. parahaemolyticus provides valuable information for developing strategies based on molecular mechanisms that inhibit these proteins, which may be useful therapeutic targets for assisting the shrimp and aquaculture industry.

Evaluation of the productive and physiological responses of Litopenaeus vannamei infected with WSSV and fed diets enriched with Dunaliella sp.

An experimental investigation was performed to evaluate the productive and physiological responses of Litopenaeus vannamei that were infected with WSSV and fed diets enriched with Dunaliella sp., which had a high ß-carotene content induced by nitrogen reduction in the culture medium. A basal diet containing 35% crude protein and experimental diets T1 and T2, which included 1% and 2% microalgae meal, respectively, were evaluated. Positive (infected juveniles) and negative (non-infected) controls were also evaluated. Survival was significantly higher (80%) in the two treatment groups compared to the positive control group (56%). In the negative control group, survival was 100%. Some variation was recorded for hemolymph metabolites among treatments and at distinct times post-infection; although the tendencies were not clear, some metabolites (glucose and triglycerides) appeared to decrease on the last days of the trial, probably due to their use as energy for the shrimp to thrive despite the infection. The results of the study suggest a positive effect of the dietary inclusion of Dunaliella meal on shrimp survival and an unclear effect on hemolymph metabolites.

World aquaculture: environmental impacts and troubleshooting alternatives.

Aquaculture has been considered as an option to cope with the world food demand. However, criticisms have arisen around aquaculture, most of them related to the destruction of ecosystems such as mangrove forest to construct aquaculture farms, as well as the environmental impacts of the effluents on the receiving ecosystems. The inherent benefits of aquaculture such as massive food production and economical profits have led the scientific community to seek for diverse strategies to minimize the negative impacts, rather than just prohibiting the activity. Aquaculture is a possible panacea, but at present is also responsible for diverse problems related with the environmental health; however the new strategies proposed during the last decade have proven that it is possible to achieve a sustainable aquaculture, but such strategies should be supported and proclaimed by the different federal environmental agencies from all countries. Additionally there is an urgent need to improve legislation and regulation for aquaculture. Only under such scenario, aquaculture will be a sustainable practice.

Production response and digestive enzymatic activity of the Pacific white shrimp Litopenaeus vannamei (Boone, 1931) intensively pregrown in microbial heterotrophic and autotrophic-based systems.

Shrimp postlarvae were reared into different microcosm systems without water exchange; a traditional system based on simple fertilization to improve microalgae concentration (control), an autotrophic system (AS) based on the promotion of biofloc and biofilm by the addition of fertilizer and artificial substrates and a heterotrophic system (HS) based on the promotion of heterotrophic bacteria by the addition of nitrogenous and carbonaceous sources and artificial substrates. Better growth performance and survival were registered in shrimp from the AS and HS compared to the control. Feed conversion ratios were below 0.7 for all treatments, but AS and HS were significantly lower than the control. Regarding digestive performance, no significant differences were observed for trypsin, amylase and lipase activities among AS and control shrimp; however, shrimp from HS showed a higher trypsin and amylase activities, suggesting a higher digestive activity caused by the presence of microbial bioflocs. The presence of biofilm and bioflocs composed by either autotrophic or heterotrophic organisms in combination with formulated feed improved the growth performance and survival of shrimp. Apparently, such combination fits the nutritional requirements of shrimp.