Mapping Microbial Capacities for Bioremediation: Genes to Genomics

Abstract

Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close to its baseline. In the process, the driving force is the available microbial genetic degradative capabilities, which are supported by required nutrients so that the desired expression of these capabilities could be exploited in favour of removal of pollutants. With genomics tools not only the available abilities could be estimated but their dynamic performance could also be established. These tools are now playing important role in bioprocess optimization, which not only derive the bio-stimulation plans but also could suggest possible genetic bio-augmentation options.

Introduction

Ecosystem services irrespective of environmental matrix are driven and decided by the key nutrient balancing modules of the biogeochemical cycles [1, 2]. This scenario gets affected by nutrient shocks due to anthropogenic activities, which in most cases could be considered as pollutants [3, 4]. Under this stressed environment with additional organic carbon as nutrients, the dynamics of community shifts and depending upon the organic loading the enrichment process starts. It creates new composition of microbial community; and the analysis of such communities in the last decades has seen paradigm shifts due to computational tools with capacity to not only generate large amount of quality data but can also efficiently process these data (Fig. 1) [5–14].

Fig. 1.

The dynamics of bacterial community metabolic shifts

Biodegradation and Bioremediation Approaches

In carbon (C) limiting environmental conditions, the bacteria use autotrophic mode of survival with capacity to utilize carbon dioxide as sole of C source [15]. However, the environmental matrix mostly provides the heterotrophic mode of survival for bacteria; and extension of this capacity for utilization of C sources entering due to anthropogenic activity in different ecosystems are considered as biodegradation. The introduction of such pollutants impacts the baseline of any ecosystem [16]. The overall process of bringing the baseline to almost its original state is considered as a process of bioremediation [17]. The bioremediation process undergoes different layers of microbial community turn over while removing the undesired organic C from the ecosystem [18, 19]. At the same time, the scale of operation in bioremediation demands segregation of different process elements and its optimization [20].

Microbes with Desired Catabolic Functions

One of the main components of any bioremediation process is the availability of microbes with desired catabolic functions. This involves the rigorous selection process where the environmental contaminated samples with target pollutants are used as initial inoculum; and through a designed enrichment process the desired microbes with catabolic potentials are selected [21–41]. However, depending upon the contamination and types of pollutants the process also leads to isolation of variety of microbes from same sample or some time even same enrichment system [42, 43]. The whole genome sequencing options provide the better understanding about the isolated strain, including its flexible multi substrate utilization capacities [44, 45].

Unfolding Bio-degradative Genetic Capacities

The genome sequencing approach has annotated the understanding of microbial capacities and allowed better exploitation of physiological capacities [45, 46]. For example, a bacterium having capacity to utilize naphthalene as C source, on complete genome annotation suggested the possible other aromatic ring degradation pathways with tolerance to different metal ions [47]. In silico genome annotation and analysis approach also helps in reducing the time required for analysis of physiological behaviour of typical isolate and utilizing its genetic information in developing tracking or sensing tools [48–52].

Complexities in Regulation of Desired Physiology

The bioprocess optimization is one of the most important steps in effective bioremediation, which could work in the presence or absence of oxygen [20]. Depending upon the organic loading and desired product, the design and operation of the bioreactor could be envisaged [53]. The second important criteria is that which type of bacteria, consortia or community is required with the bioreactor configuration and desired metabolic pathways [54–62]; and sometimes to achieve maximum output from the strains, a simulation laboratory experiments are designed which are critical for optimization of operational conditions. These can be applied at a pilot or full-scale level [63–66]. To enhance the desired expression of degradative phenotype the induction of metabolic pathways with required microbial density plays a key role; for example, typical levels of microbial density wherein the quorum sensing phenomenon induces the desired functions observed to be associated with optimum performance of bioreactors with granulation of microbial community [67–70].

Monitoring Bacteria in Environments

The efficiency of monitoring process depends on the assessment of abundance of functional genotypes, which can be affectively monitored by using polymerase chain reaction, a tool which targets the gene(s) in question [71–81]. However, with next generation sequencing (NGS) approach the microbial community tracking has changed completely; and with comparative details it provides temporal and spatial data [82, 83]. However, the efficiency of this analysis is decided by the choice of computational tool applied; or depending upon the analysis plan even the novel pipeline must be devised for better understanding of the system variables [84]. This issue is highly relevant in case of closely related genera or species, where further analysis of taxonomically relevant gene such as 16Sr RNA gene requires the case specific algorithm [85–92].

Metagenomics: Analysing Microbial Communities

Metagenomics involves the analysis of total DNA associated with any ecological sample [5]. The reliability of analysis is decided by the efficiency of extractions of total representative DNA of the sample [93–96]. The developed metagenome extraction techniques have been evaluated and applied with different samples [97–103]. There are different pipelines available for analysis of metagenomic data generated by NGS [104]; however, the microbial community structures are so complex that analysis must be driven by different possible hypothesis and their validation [105]. For example, by planning of novel sequence mining approach a unique class of enzymes can be targeted from the data generated from a bioreactor [106, 107], or even by analysing the metagenome data generated from the reactor an operational-conditions could be planned or revised [108, 109]. However, the challenges are there to understand the community colonization with highly persistent pollutants [110–112]. In addition to this, metagenomics approach can help in developing the valorisation projects such as utilization of agricultural residues [113–118].

Bio-augmentation and Bio-stimulation

The biological waste treatment systems are cost effective, but their efficiencies are directly proportional to performance of the microbial community associated with the specific system. Bio-augmentation is mostly carried out for balancing the nutrients, wherein a specific bacterial strain or consortium is introduced into the degradative system [119–121]. This essentially genetically bio-augments the required degradative capacity which also can be achieved using bacterial strain flexible with degradative capacity [122]. Bio-stimulation of microbial community can be achieved either by balancing the nutrients, if the required C:N (Nitrogen):P (Phosphorus) ratio in the ecosystem is not supporting the degradation kinetics [123–125], or some intermediates of pathways can be introduced in the system which can induce the expression of required genes [66, 67, 126]. The application of bio-stimulation and bio-augmentation is now a days applied extensively to different types contaminated ecosystem particularly associated with persistent organic pollutants [127–131]. To further enhance the effective strategy, the plant–microbe interactions are also being applied wherein balancing of nutrients with the network of designed rhizospheric population further creates the environment for effective degradation kinetics [132–136]. Another challenge in bioremediation is the sites with almost no nutrients such as rocky land, sand or arid ecosystems; and in such environments, the nutrient balancing with organic load of pollutants affects the bioremediation process. In such cases, the augmentation of bacteria which can bring out the C or N fixation, efficient utilization of pollutants with supplementation of P can favour the remediation measures [137–140].

Bioremediation Challenges and Future Perspective

The microbial community data generated through NGS tools and further analysed by computational analysis suggest that the diversity of most of the ecosystem is still not completely explored [5, 18, 44, 141]. Bioremediation approach to an extent is relatively uncontrolled enrichment process under the pressure of few identified contaminates [3, 17, 142]. Hence, initial assessment and diagnosis of system is crucial, which will guide the work plan for enrichment of desired microbes to address the detail work element the bio-stimulation or bio-augmentation process can be recruited to overall remedial approach [143, 144]. Based on that the possible biological interactions associated with remedial site could be envisaged. This matrix finally represents dynamics of multi species—multi substrate system [119, 145–147], and hence, amending the system with desired genotypes some time becomes mandatary [100, 122]. Second approach could be training the bacterial strains before releasing in the environment and understanding of its functional modules; and possible effects on the strain due to other microbial species, metabolites and/or inhibitors [20, 101, 148–158]. Once this is established the selected bioprocess can be designed and extended for field scale operation. However, the challenges will be always there if the site is also having metal ions as contaminants, which may require some innovative approaches [159–162]. The complexities in biological process requires redefining the thinking process where the environmental factors with dynamics of metabolite continuously not only defines the community structure but also their expression profiles [163, 164].