Isolation and identification of metallotolerant bacteria with a potential biotechnological application.

Mining has led to severe environmental pollution in countries with exhaustive mining production and inadequate industrial waste regulation. Microorganisms in contaminated sites, like mine tailings, have adapted to high concentrations of heavy metals, developing the capacity of reducing or removing them from these environments. Therefore, it is essential to thoroughly characterize bacteria present in these sites to find different ways of bioremediation. In this regard, in this study, an enrichment and isolation procedure were performed to isolate bacteria with lower nutritional requirements and high tolerance to Cu(II) and Fe(II) from two Sonoran River basin mining tails. Two Staphylococcus species and a Microbacterium ginsengisoli strain were isolated and identified from the San Felipe de Jesús mining tail. Also, three strains were isolated from the Nacozari de García mining tail: Burkholderia cenocepacia, Sphingomonas sp. and Staphylococcus warneri. Significant microbiological differences were found between the two sites. All these species exhibited tolerance up to 300 mg/L for Cu (II)-Fe (II) solutions, indicating their capacity to grow in these conditions. Moreover, a consortium of isolated bacteria was immobilized in two different biocomposites and the biocomposite with larger pore size achieved greater bacterial immobilization showcasing the potential of these bacteria in biotechnological applications.

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.

Synthesis and Cytotoxicity Studies of Br-Substituted Salphen Organic Compounds.

We present the synthesis and characterization of organic Salphen compounds containing bromine substituents at the para/ortho-para positions, in their symmetric and non-symmetric versions, and describe the X-ray structure and full characterization for the new unsymmetrical varieties. We report for the first time antiproliferative activity in metal-free brominated Salphen compounds, by evaluations in four human cancer cell lines, cervix (HeLa), prostate (PC-3), lung (A549) and colon (LS 180) and one non-cancerous counterpart (ARPE-19). We assessed in vitro cell viability against controls using the MTT assay ((3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide)) and determined the concentration required for 50 % growth inhibition (IC50 ), together with their selectivity vs. non-cancerous cells. We found promising results against prostate (9.6 µM) and colon (13.5 µM) adenocarcinoma cells. We also found a tradeoff between selectivity (up to 3-fold vs. ARPE-19) and inhibition, depending upon the symmetry and bromine-substitution of the molecules, showing up to 20-fold higher selectivity vs. doxorubicin controls.

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei.

The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components' significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities' structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction's bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp's gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

Removal of nickel(II) from wastewater using a zeolite-packed anaerobic bioreactor: Bacterial diversity and community structure shifts.

In recent years, overexploited industrialization and urbanization activities have led to significant amounts of heavy metals released into the environment. Metal ion contamination of water, especially with toxic metals such as nickel(II) [Ni(II)], which is extensively applied in the electroplating industry, has been a serious problem. The aim of the present study was to evaluate the Ni(II) removal from real industrial wastewater using a 2 L, lab-scale, up-flow, anaerobic, zeolite-packed bioreactor inoculated with a heterotrophic consortium as the bioadsorbent. High-throughput sequencing of 16S rRNA genes revealed significant shifts in their bacterial diversity and structural composition along the bioreactor treatment location, where the bacterial genus was dominated by Kosmotogae followed by Firmicutes as Ruminococcus and Clostridium. However, Fervidobacterium and the Geobacter genus were absent at the end of the bioreactor treatment, suggesting that they play a key role in the beginning of Ni(II) removal anaerobic treatment. The physico-chemical results revealed that the Ni(II) removal rate was 99% for 250-500 ppm metal tested, with an efficient alkalinity rate and high production of biogas, which confirmed that anaerobic digestion of microorganisms was successfully performed through the process. Finally, this anaerobic bioreactor configuration offers an accessible and ecofriendly high-rate metal removal strategy from mining and electroplating effluents.

The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development.

This work aimed to evaluate the link between the occurrence/abundance of Vibrio populations and bacterial composition in shrimp's intestine (Litopenaeus vannamei) during post-larval ontogenetic development and in its culture water, and the correlation of these with environmental parameters. The total and metabolically active populations of Vibrio in the digestive tract of shrimp during its post-larval development were analysed using quantitative PCR (qPCR) and reverse transcription qPCR targeting the 16S rRNA gene sequence. A lab-scale shrimp bioassay was performed for 80 days in a recirculating aquarium under strictly controlled conditions. The results indicate that the Vibrio population from shrimp's gut is associated with its developmental stage and the environment. Multivariate analyses revealed that the presence of Vibrio spp. drove the studied system, but their metabolically active performance was related to earlier developmental stages in an aqueous environment. Also, the samples taken from water of culture units to compare the influence of the aquatic environment on the intestinal microbial community during shrimp's ontogenetic development showed significant differences. Finally, our results revealed that Vibrio is an important member of shrimp's gut microbiota; however, its metabolic activity seems to be highly regulated, possibly by the host and by the rest of the microbiota.

A novel process of the isolation of nitrifying bacteria and their development in two different natural lab-scale packed-bed bioreactors for trichloroethylene bioremediation.

Trichloroethylene (TCE) is a carcinogenic compound that is commonly present in groundwater and has been detected in drinking water sources for Mexican towns in the Mexico-US border area. Nitrifying bacteria, such as Nitrosomonas europaea, have been shown to be capable of degrading halogenated compounds, including TCE, but it is difficult to obtain high cell concentrations of these bacteria. The aim of the present study was to generate biomass of a nitrifying bacterial consortium from the sludge of an urban wastewater treatment plant (WWTP) and evaluate its capacity to biodegrade TCE in two different natural lab-scaled packed bed bioreactors. The consortium was isolated by a novel method using a continuous stirred-tank bioreactor inoculated with activated sludge from the Domos WWTP located in Cd. Obregón, Sonora, Mexico. The bioreactor was fed with specific media to cultivate ammonia-oxidizing bacteria at a dilution rate near the maximum specific growth rate reported for Nitrosomonas europaea. Optical density and suspended solids measurements were performed to determine the culture biomass production, and the presence of inorganic nitrogen species was determined by spectrophotometry. The presence of nitrifying ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was confirmed by PCR amplification, and biofilm formation was observed by scanning electron microscopy. Batch-scale experiments confirmed the biodegradative activity of the isolated consortium, which was subsequently fixed in an inorganic carrier as zeolite and a synthetic carrier such as polyurethane to both be used as lab-scale packed-bed bioreactors, with up to 58.63% and 62.7% of TCE biodegradation achieved, respectively, demonstrating a possible alternative for TCE bioremediation in environmental and engineering systems.

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.

Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions.

There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate complex, non-additive effects on ecosystems functioning. However, how the chronology of disturbances can affect ecosystems functioning is unknown even though there is increasing evidence that community assembly history dictates ecosystems functioning. Here, we experimentally examined the importance of the disturbances chronology in modulating the resilience of soil microbial communities and N-cycle related functions. We studied the impact of 3-way combinations of global change related disturbances on total bacterial diversity and composition, on the abundance of N-cycle related guilds and on N-cycle related activities in soil microcosms. The model pulse disturbances, i.e., short-term ceasing disturbances studied were heat, freeze-thaw and anaerobic cycles. We determined that repeated disturbances of the same nature can either lead to the resilience or to shifts in N-cycle related functions concomitant with diversity loss. When considering disturbances of different nature, we demonstrated that the chronology of compounded disturbances impacting an ecosystem determines the aggregated impact on ecosystem properties and functions. Thus, after 3 weeks the impact of the 'anoxia/heat/freeze-thaw' sequence was almost two times stronger than that of the 'heat/anoxia/freeze-thaw' sequence. Finally, we showed that about 29% of the observed variance in ecosystem aggregated impact caused by series of disturbances could be attributed to changes in the microbial community composition measured by weighted UniFrac distances. This indicates that surveying changes in bacterial community composition can help predict the strength of the impact of compounded disturbances on N-related functions and properties.

Effectiveness of ecological rescue for altered soil microbial communities and functions.

Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential of manipulating soil microbial communities for the recovery of ecosystem functioning. We used a reciprocal transplant design in experimentally altered microbial communities to investigate the effectiveness of introducing microbial communities in degraded soil ecosystems to restore N-cycle functioning. Microbial diversity loss resulted in alternative compositional states associated with impaired N-cycle functioning. Here, the addition of complex microbial communities to these altered communities revealed a pivotal role of deterministic community assembly processes. The diversity of some alternative compositional states was successfully increased but without significant restoration of soil N-cycle functioning. However, in the most degraded alternative state, the introduction of new microbial communities caused an overall decrease in phylogenetic diversity and richness. The successful soil colonization by newly introduced species for some compositional states indicates that priority effects could be overridden when attempting to manipulate microbial communities for soil restoration. Altogether, our result showed consistent patterns within restoration treatments with minor idiosyncratic effects. This suggests the predominance of deterministic processes and the predictability of restoration trajectories, which could be used to guide the effective management of microbial community assemblages for ecological restoration of soils.

New concepts of microbial treatment processes for the nitrogen removal: effect of protein and amino acids degradation.

High concentrations of proteins and amino acids can be found in wastewater and wastewater stream produced in anaerobic digesters, having shown that amino acids could persist over different managements for nitrogen removal affecting the nitrogen removal processes. Nitrogen removal is completely necessary because of their implications and the significant adverse environmental impact of ammonium such as eutrophication and toxicity to aquatic life on the receiving bodies. In the last decade, the treatment of effluents with high ammonium concentration through anammox-based bioprocesses has been enhanced because these biotechnologies are cheaper and more environmentally friendly than conventional technologies. However, it has been shown that the presence of important amounts of proteins and amino acids in the effluents seriously affects the microbial autotrophic consortia leading to important losses in terms of ammonium oxidation efficiency. Particularly the presence of sulfur amino acids such as methionine and cysteine has been reported to drastically decrease the autotrophic denitrification processes as well as affect the microbial community structure promoting the decline of ammonium oxidizing bacteria in favor of other phylotypes. In this context we discuss that new biotechnological processes that improve the degradation of protein and amino acids must be considered as a priority to increase the performance of the autotrophic denitrification biotechnologies.

Archaeal diversity in biofilm technologies applied to treat urban and industrial wastewater: recent advances and future prospects.

Biological wastewater treatment (WWT) frequently relies on biofilms for the removal of anthropogenic contaminants. The use of inert carrier materials to support biofilm development is often required, although under certain operating conditions microorganisms yield structures called granules, dense aggregates of self-immobilized cells with the characteristics of biofilms maintained in suspension. Molecular techniques have been successfully applied in recent years to identify the prokaryotic communities inhabiting biofilms in WWT plants. Although methanogenic Archaea are widely acknowledged as key players for the degradation of organic matter in anaerobic bioreactors, other biotechnological functions fulfilled by Archaea are less explored, and research on their significance and potential for WWT is largely needed. In addition, the occurrence of biofilms in WWT plants can sometimes be a source of operational problems. This is the case for membrane bioreactors (MBR), an advanced technology that combines conventional biological treatment with membrane filtration, which is strongly limited by biofouling, defined as the undesirable accumulation of microbial biofilms and other materials on membrane surfaces. The prevalence and spatial distribution of archaeal communities in biofilm-based WWT as well as their role in biofouling are reviewed here, in order to illustrate the significance of this prokaryotic cellular lineage in engineered environments devoted to WWT.

Comparative analysis of the enzyme activities and the bacterial community structure based on the aeration source supplied to an MBR to treat urban wastewater.

A comparative analysis was performed in a pilot-scale membrane bioreactor (MBR) treating urban wastewater supplied with either pure oxygen (O2) or air, to assess the influence of each aeration source on the diversity and activity of the bacterial communities in the sludge. The MBR was operated in three experimental stages with different concentrations of volatile suspended solids (VSS) and temperature, and under both aeration conditions. α-Glucosidases, proteases, esterases and phosphatases were tested as markers of organic matter removal in the sludge, and the diversity of the bacterial community was analysed by fingerprinting (temperature-gradient gel electrophoresis of partially-amplified 16S-rRNA genes). Redundancy analysis (RDA) revealed that temperature and VSS concentration were the only factors that significantly influenced the levels of enzyme activities and the values of both the Shannon-Wiener diversity index (H') and the functional organisation index (Fo), while the bacterial community structure experienced significant changes depending on the aeration source supplied in each experimental stage.

Comparative analysis of the bacterial diversity in a lab-scale moving bed biofilm reactor (MBBR) applied to treat urban wastewater under different operational conditions.

Different types of carriers were tested as support material in a lab-scale moving bed biofilm reactor (MBBR) used to treat urban wastewater under three different conditions of hydraulic retention time (HRT) and carrier filling ratios (FR). The bacterial diversity developed on the biofilms responsible of the treatment was studied using a cultivation-independent approach based on the polymerase chain reaction-temperature gradient gel electrophoresis technique (PCR-TGGE). Cluster analysis of TGGE fingerprints showed significant differences of community structure dependent upon the different operational conditions applied. Redundancy analysis (RDA) was used to determine the relationship between the operational conditions (type of carrier, HRT, FR) and bacterial biofilm diversity, demonstrating a significant effect of FR=50%. Phylogenetic analysis of PCR-reamplified and sequenced TGGE bands revealed that the prevalent Bacteria populations in the biofilm were related to Betaproteobacteria (46%), Firmicutes (34%),Alphaproteobacteria (14%) and Gammaproteobacteria (9%).

Bacterial community structure and enzyme activities in a membrane bioreactor (MBR) using pure oxygen as an aeration source.

A pilot-scale membrane bioreactor was used to treat urban wastewater using pure oxygen instead of air as a source of aeration, to study its influence on bacterial diversity and levels of enzyme activities (acid and alkaline phosphatases, glucosidase, protease, and esterase) in the sludge. The experimental work was developed in two stages influenced by seasonal temperature. Operational parameters (temperature, pH, BOD5, COD, total and volatile suspended solids) were daily monitored, and enzyme activities measured twice a week. Redundancy analysis (RDA) was used to reveal relationships between the level of enzyme activities and the variation of operational parameters, demonstrating a significant effect of temperature and volatile suspended solids. Bacterial diversity was analyzed by temperature-gradient gel electrophoresis of PCR-amplified partial 16S rRNA genes. Significant differences in community structure were observed between both stages. Sequence analysis revealed that the prevalent Bacteria populations were evolutively close to Alphaproteobacteria (44%), Betaproteobacteria (25%) and Firmicutes (17%).

Analysis of microbial communities developed on the fouling layers of a membrane-coupled anaerobic bioreactor applied to wastewater treatment.

The structure of the biofouling layers formed on a pilot-scale membrane-coupled upflow anaerobic sludge blanket bioreactor (UASB) used to treat urban wastewater was analyzed by scanning electron microscopy and electron-dispersive X-ray microanalysis. For comparison, control samples of the membranes were fed either UASB effluent or raw wastewater in a laboratory-scale experiment. Microbial diversity in the fouling materials was analyzed by temperature gradient gel electrophoresis (TGGE) combined with sequence analysis of partial 16S rRNA. Significant differences in structure of the Bacteria communities were observed amongst the different fouling layers analyzed in the UASB membranes, particularly following a chemical cleaning step (NaClO), while the Archaea communities retained more similarity in all samples. The main Bacteria populations identified were evolutively close to Firmicutes (42.3%) and Alphaproteobacteria (30.8%), while Archaea were mostly affiliated to the Methanosarcinales and Methanospirillaceae. Sphingomonadaceae-related bacteria and methanogenic Archaea were persistently found as components of biofouling, regardless of chemical cleaning.