Interspecific interactions in mixed microbial cultures in a biodegradation perspective

Dynamics of effluent treatment plant during commissioning of activated sludge process unit

Industrial effluent treatment plants (ETPs) are very important in protecting the environment and different life forms from harmful industrial waste. Hence, the efficiency of ETPs must be regularly monitored, particularly after major repair or replacement work. Present study evaluated the performance of an ETP over a period of 4 months, during which aeration tank (T1) of the activated sludge unit was replaced with a new one (T2). System had to be maintained operational during this transition, which warranted close monitoring of the system performance due to the daily load of hazardous industrial wastewater. Analysis showed that the raw wastewater was highly variable in composition and contained many hazardous organic and inorganic pollutants, such as heavy metals, bisphenol A and cyanoacetylurea. It showed significant toxicity against HepG2 cells in vitro. However, the ETP was found to successfully treat and detoxify the wastewater. Denaturing gradient gel electrophoresis (DGGE) analysis showed large temporal fluctuations in the ETP microbial community, which is consistent with the variable composition of wastewater. It indicated that functional stability of the ETP was not associated with stability of the microbial community, probably due to high microbial biodiversity and consequently high functional redundancy. In conclusion, the CETP showed consistent level of detoxification and microbial community dynamics after switching to T2, indicating successful development, acclimatization and commissioning of T2.

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes.

Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.

Potential of fungal co-culturing for accelerated biodegradation of petroleum hydrocarbons in soil

The potential of fungal co-culture of the filamentous Pestalotiopsis sp. NG007 with four different basidiomycetes--Trametes versicolor U97, Pleurotus ostreatus PL1, Cerena sp. F0607, and Polyporus sp. S133--for accelerating biodegradation of petroleum hydrocarbons (PHCs) was studied using three different physicochemical characteristic PHCs in soil. All the combinations showed a mutual intermingling mycelial interaction on the agar plates. However, only NG007/S133 (50/50) exhibited an optimum growth rate and enzymatic activities that supported the degradation of asphalt in soil. The co-culture also degraded all fractions at even higher concentrations of the different PHCs. In addition, asphaltene, which is a difficult fraction for a single microorganism to degrade, was markedly degraded by the co-culture, which indicated that the simultaneous biodegradation of aliphatic, aromatic, resin, and asphaltene fractions had occurred in the co-culture. An examination of in-vitro degradation by the crude enzymes and the retrieval fungal culture from the soil after the experiment confirmed the accelerated biodegradation due to enhanced enzyme activities in the co-culture. The addition of piperonyl butoxide or AgNO3 inhibited biodegradation by 81-99%, which demonstrated the important role of P450 monooxygenases and/or dioxygenases in the initial degradation of the aliphatic and aromatic fractions in PHCs.

Bioresources for control of environmental pollution

Environmental pollution is one of the biggest threats to human beings. For practical reasons it is not possible to stop most of the activities responsible for environmental pollution; rather we need to eliminate the pollutants. In addition to other existing means, biological processes can be utilized to get rid of toxic pollutants. Degradation, removal, or deactivation of pollutants by biological means is known as bioremediation. Nature itself has several weapons to deal with natural wastage and some of them are equally active for eliminating nonnatural pollutants. Several plants, microorganisms, and some lower eukaryotes utilize environmental pollutants as nutrients and some of them are very efficient for decontaminating specific types of pollutants. If exploited properly, these natural resources have enough potential to deal with most elements of environmental pollution. In addition, several artificial microbial consortia and genetically modified organisms with high bioremediation potential were developed by application of advanced scientific tools. On the other hand, natural equilibria of ecosystems are being affected by human intervention. Rapid population growth, urbanization, and industrialization are destroying ecological balances and the natural remediation ability of the Earth is being compromised. Several potential bioremediation tools are also being destroyed by biodiversity destruction of unexplored ecosystems. Pollution management by bioremediation is highly dependent on abundance, exploration, and exploitation of bioresources, and biodiversity is the key to success. Better pollution management needs the combined actions of biodiversity conservation, systematic exploration of natural resources, and their exploitation with sophisticated modern technologies.

Interactions in the microbiome: communities of organisms and communities of genes

A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'

Fungal-bacterial consortia increase diuron degradation in water-unsaturated systems

Bioremediation of pesticide-polluted soil may be more efficient using mixed fungal-bacterial cultures rather than the individual strains alone. This may be due to cooperative catabolism, where the first organism transforms the pollutant to products which are then used by the second organism. In addition, fungal hyphae may function as transport vectors for bacteria, thereby facilitating a more effective spreading of degrader organisms in the soil. A more rapid mineralization of the phenylurea herbicide diuron was found in sand with added microbial consortia consisting of both degrading bacteria and fungi. Facilitated transport of bacteria by fungal hyphae was demonstrated using a system where herbicide-spiked sand was separated from the consortium by a layer of sterile glass beads. Several fungal-bacterial consortia were investigated by combining different diuron-degrading bacteria (Sphingomonas sp. SRS2, Variovorax sp. SRS16, and Arthrobacter globiformis D47) and fungi (Mortierella sp. LEJ702 and LEJ703). The fastest mineralization of (14)C-labeled diuron was seen in the consortium consisting of Mortierella LEJ702, Variovorax SRS16, and A. globiformis D47, as measured by evolved (14)CO2. In addition, the production of diuron metabolites by this consortium was minimal. Analyses of 16S rDNA suggested that bacteria were transported more efficiently by LEJ702 than by LEJ703. Finally, it was determined that the fungal growth differed for LEJ702 and LEJ703 in the three-member consortia. This study demonstrates new possibilities for applying efficient fungal-bacterial consortia for bioremediation of polluted soil.

Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture

Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data.

Characterization of pbt genes conferring increased Pb2+ and Cd2+ tolerance upon Achromobacter xylosoxidans A8

The cluster of pbtTFYRABC genes is carried by plasmid pA81. Its elimination from Achromobacter xylosoxidans A8 resulted in increased sensitivity towards Pb(2+) and Cd(2+). Predicted pbtTRABC products share strong similarities with Pb(2+) uptake transporter PbrT, transcriptional regulator PbrR, metal efflux P1-ATPases PbrA and CadA, undecaprenyl pyrophosphatase PbrB and its signal peptidase PbrC from Cupriavidus metallidurans CH34. Expression of pbtABC or pbtA in a metal-sensitive Escherichia coli GG48 rendered the strain Pb(2+)-, Cd(2+)- and Zn(2+)-tolerant and caused decreased accumulation of the metal ions. Accumulation of Pb(2+), but not of Cd(2+) or Zn(2+), was promoted in E. coli expressing pbtT. Additional genes of the pbt cluster are pbtF and pbtY, which encode the cation diffusion facilitator (CDF)-like transporter and a putative fatty acid hydroxylase of unknown function, respectively. Expression of pbtF did not confer increased metal tolerance upon E. coli GG48, although the protein showed measurable Pb(2+)-efflux activity. Unlike the pbtT promoter, promoters of pbtABC, pbtF and pbtY contain features characteristic of promoters controlled by metal-responsive transcriptional regulators of the MerR family. Upregulation of pbtABC, pbtF and pbtY upon Pb(2+), Cd(2+) and Zn(2+) exposure was confirmed in wild-type Achromobacter xylosoxidans A8. Gel shift assays proved binding of purified PbtR to the respective promoters.

A novel approach to stimulate the biphenyl-degrading potential of bacterial community from PCBs-contaminated soil of e-waste recycling sites

SRpf, culture supernatants from Micrococcus luteus containing the resuscitation-promoting factor (Rpf), was used to enhance the biphenyl-degrading capability of potential microorganisms. The obtained results suggest that the enrichment culture produced by the addition of SRpf (enrichment culture treatment group, ECT) enhanced the biphenyl degradation efficiency, cell growth and bacterial diversity significantly. Biphenyl at concentration of 1500 mg/L was almost completely degraded in 24 h using SRpf at a dosage of 15% (v/v). Six strains unique to the ECT were isolated in pure cultures. This study provides a new insight into bacterial degradation of biphenyl for PCBs-bioremediation, and could be developed as a novel efficient method for obtaining highly desirable pollutant-degrading microorganisms.

Molecular fingerprinting of bacterial communities in enriched azo dye (Reactive Violet 5R) decolorising native acclimatised bacterial consortia

Reactive Violet 5R (RV5R) decolorising acclimatised bacterial consortia were enriched from industrial effluent contaminated and pristine samples from Gujarat, India on several different media. Twelve acclimatised consortia were selected for the study which were able to decolorise 100mg/L RV5R in 30 h under shaking or static conditions. Eubacterial diversity was studied by 16S rRNA gene based culture-independent methods, using HaeIII and Hinf1 enzymes for ARDRA and V3 region based DGGE analysis, forming total 6 clusters in both analysis. Decolorised end products of all the consortia were analysed by FTIR showing cleavage of the azo bond and group modifications. GC-MS data of dye decolorised end products of Gly consortium obtained from hydrocarbon contaminated soil demonstrated benzene ring cleavage activity. Present study suggests that enrichment of acclimatised consortia under different conditions can result in diverse microbial communities that differentially degrade RV5R and can provide rich source of dye decolorising strains.