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River Health and Ecology in South
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Abstract The aquatic environment is the governance system for sustenance of life
on earth. Nowadays, aquatic bodies are under serious threat throughout the globe
due to industrialization and other anthropogenic activities. Pollution has been a
stress for aquatic organisms, plants, and humans along with the pressure from
changing climatic conditions. Freshwater is only 2.5% of the total water available
on the earth and out of total freshwater 1.2 is only available on the surface rest are
either in glacial form or in groundwater. The protection of high-quality freshwater
is essential to maintain a healthy riverine ecosystem. This is an approach to imple-
ment advanced scientific technologies such as; microbiology, molecular biology,
biotechnology, bioinformatics, metagenomics and other omics platforms to observe,
analyze, and manage the information obtained from aquatic ecosystems to develop
superior biotechnological methods to maintain the quality of freshwater.
1 Introduction
Water is necessary for sustenance of life on earth and river is the major source of it.
Freshwater is only 2.5% of the total water available on the earth and out of total
freshwater 1.2 is only available on the surface rest is either in glacial form or in
groundwater. India is bestowed with 29,000 km length of river network which not
only provides water for a human beings for their daily requirement but also pro-
vides, “fish” as a source of animal nutrition, aquatic plants along with water for
irrigation to grow various crops and vegetables. Rivers play a significant role in
Indian tradition and culture. They are the lifeblood of the majority of people in
towns, cities, villages and many of them are considered sacred, with people taking
holy baths in rivers during festivals. Bathing, navigation, public supply, drinking,
fishing, and irrigation are only a few of the water uses along each river stretch. At
the same time, it serves as a receptacle for the discharge of urban sewage, industrial
effluent, and solid waste dumping. River Pollution is addition of something which
changes the natural quality or substances which make the water unfavorable for life
in river water (Wisdom 1966). River pollution is having a long history and presently,
it is exploited to a higher degree. During the eighteenth century, many industries
came to Europe and pollution growth was also there. All the waste from the indus-
tries and the urban area is discharged into rivers either without treatment or with
partial treatment. Many acts came into force during the same time to save the river
water and fisheries from pollutants from different sources. Gas Works clause Act
1847, Salmon Fishing act 1861 and 1865; Setting up of Royal commission on the
prevention of river pollution, 1865, River pollution act 1876, 1890; Royal commis-
sion on Sewage disposal, 1898 but no act was passed in parliament; 1923, Salmon
fishing act extended to trout are few of the acts to protect water resources and
aquatic organisms. The Water (Prevention and Control of Pollution) Act of 1974
aims to protect the water quality of different water bodies that have been identified
as best uses.
Now a days, industries are the major problem for environmental pollution. It
releases a wide range of harmful substances, solid wastes, microbes, and gases of
different types into our immediate ecosystems, such as water, air, and soil. Water
pollution has become a global problem, with developing countries bearing a dispro-
portionately high burden as a result of their growth imperatives (Inyinbor et al.
2016; Rana et al. 2017). Pollution of our water sources is a threat to humans and the
aquatic ecosystem since population growth has accelerated climatic changes
(Palmate et al. 2017). Biotechnology provides a wide range of opportunities for
addressing river pollution issues effectively. Among different biotechnological
tools, the metagenomic approach of identifying the helpful microbiome in river
sediment is one of the approaches for pollution management.
4 Role of Modern Biotechnology in the Era of River Water Pollution 65
Over the last few decades, there have been many instances of water pollution/con-
tamination caused by accidents or illegal activities all over the world. For example,
the Tuojiang River pollution incident occurred in 2014, the Songhua River benzene
pollution incident occurred in 2005, the Colorado River pollution incident occurred
in 2015, and so on. The water contamination was caused by a massive amount of
chemicals spilling into the atmosphere, resulting in a drastic increase in contami-
nants, which could have a variety of effects on the health of water bodies. Viral,
bacterial, and fungal pathogens, as well as protozoal hosts for extracellular DNA
and intracellular pathogens, were among the pollutants (e.g., antibiotic resistance
genes) (Turnbaugh et al. 2009; Qin et al. 2010). It is hard to culture these pathogens
in routine monitoring because most pathogens are fastidious, slow- growing.
Antibiotic resistance marker genes or targeted pathogens that hybridize primers or
probes engineered can be determined using culture-based molecular methods such
as qPCR (quantitative PCR). This conventional approach relies heavily on data
monitoring, which is labor intensive.
The metagenomics (DNA/16S rRNA based) method is suitable for monitoring
of microbial target (i.e., virus, bacteria, and protozoa) from polluted river water. We
came to this conclusion after reviewing the following evidence: (1) advances tech-
nologies for metagenome sequencing and (2) the accessibility and use of computa-
tional tools for metagenomic data analysis. However, it would need to further
develop to the quantitative measurements of samples, good accuracy and high reso-
lution of functional classification and phylogenetic analysis result in a mixed water
population to accurately meet the requirements of refined the monitoring of water
quality (Turnbaugh et al. 2009).
Several next generation sequencing (NGS) platforms were used for complete
metagenome sequencing, such as Ion Torrent, 454 pyrosequencing, Illumina,
Nanopore, and PacBio (Table 4.1). Longer reads (2900 bp) can be generated by
PacBio compare to the Illumina reading (50–300 bp). The generated read depends
upon the quality as well as size of the DNA template. The key distinguishing attri-
bute of these sequencing technologies is to generate a huge number of short reads
length sequencing (typically 100–300 bp per reading) per run (Aird et al. 2011;
Brandariz-Fontes et al. 2015). Also, shotgun sequencing library preparation required
approximately 400 bp DNA fragments, so no need for high quantity DNA. However,
producing reads with lengths shorter than the standard too fragmenting DNA would
also affect the efficiency of sequencing. Therefore, protocol optimization is very
important to reduce the related error levels and lapses in sequencing quality.
66 A. K. Rout et al.
improved high-quality data visualization, so that researchers can test and modify
taxonomy and practical description at various resolution levels (Arango-Argoty
et al. 2016). Whereas MOTHUR is a complete single-piece software package for
metagenome analysis and it allows to use to analyze community sequence data
(Schloss et al. 2009). TreeClimber, SONS, DOTUR, LIBSHUFF, and UniFrac have
all used MOTHUR algorithms in the past (Schloss et al. 2009). To boost the DADA
algorithm, DADA2 is a new model for Illumina amplicon errors (Callahan et al.
2016). The result of DADA2 gives a sequence table and OTUs tables. It was deter-
mined how many times the ribosomal sequence number was revised in each sample
(http://benjjneb.github.io/dada2/tutorial.html). DADA2 is a model-based technique
for correcting amplicon errors without the need for OTU construction. It aims to
find fine-scale variations in 454-sequenced amplicon data with as few false positives
as possible (Callahan et al. 2016). However, the overall workflow for river metage-
nome is shown in Fig. 4.1.
Metagenome sequencing has been documented in some rivers such as Yamuna
and Ganga (Mittal et al. 2019; Reddy and Dubey 2019; Samson et al. 2019; Behera
et al. 2020b, a; Das et al. 2020), Apies River (Abia et al. 2018), Amazon River (Ghai
et al. 2011), 11 Rivers of West and East of Norwich UK, (Reddington et al. 2020),
Bighorn River (Hamner et al. 2019), Bogota River (Ruiz-Moreno et al. 2019), James
River (Brown et al. 2015), etc. and observed that archaeal and bacterial communi-
ties across the confluence response to a variety of factors responsible for water pol-
lution, including variations in temperature, climate change, the physicochemical
parameter of water, agricultural runoff, and unregulated small-scale industry. The
information regarding the common microbes is present in the polluted water as
shown in Table 4.3. When combined with Meta-Transcriptomic data (RNA-Seq of
environmental samples), metagenomics has shed light on group function and can
provide information about the critical microbial survival in a given condition. The
microbes identified from metagenomic analysis on biodegrading microbes will help
in industrial use of river water pollution abetment.
Biofilms are multifaceted permeable structures and one of the greatest tolerant com-
munities belonging to the aquatic ecosystem. Ecologically efficient strains of bacte-
ria, algae, and fungi contribute to its structural components. Aerobic microbes and
algal components in biofilms free aquatic ecosystems from excessive nutrient load-
ings and pollutants by using them as carbon sources like potential degrading agents
(Sgountzos et al. 2006). They can be utilized in the bioremediation of heavy metals
and also as pollution bioindicators. Different studies have evaluated the role of
biofilm-derived microorganisms to remove or reduce the effect of several contami-
nants from polluted water in an environment friendly way (Table 4.4). The applica-
tions are cost-effective and hold great future scopes. Microorganisms inside biofilms
use the basic cellular machinery of assimilation, adsorption, and biodegradation to
70 A. K. Rout et al.
Table 4.4 Biofilm-derived microorganisms to remove or reduce the effect of several contaminants
from polluted water
Biofilm-derived microbial isolates Environmental Benefits References
Burkholderiae sp., Sphingomonas Pseudomonas MT1 isolate El-Rakaiby et al. (2013)
sp., pseudomonas sp., and showed the highest
Chryseomonas sp. biodegradation capacity
(1700 mg/L of phenol and
3000 mg/L of pyridine)
Aeromonas caviae, fusarium Significant reduction in BOD and El Bestawy et al.
udum, pseudomonas stutzeri, COD of wastewater (2014), Rozitis and
Sphingobacterium thalpophilum, Strade (2015)
and Rhodotorula mucilaginosa
E. coli (Rz6), Bacillus Total suspended solids and total Dasgupta et al. (2013),
amyloliquefaciens (S1), and their coliform from wastewater were El Bestawy et al. (2014)
mixed culture. Pseudomonas eliminated. Pseudomonas otitidis
otitidis has been able to degrade crude oil
A. hydrophila L6, B. denitrificans Biological denitrification of Jiang et al. (2008),
B79, Thauera sp., pseudomonas wastewater and river water is Andersson (2009), Sriu
stutzeri and Rheinheimera enhanced by these microbes Naik and Pydi Setty
pacifica (2011)
Azoarcus sp., Thauera sp., Heterotrophic nitrification in Wang et al. (2014), Ma
Comamonas sp. and Paracoccus aquatic ecosystems. et al. (2015), Cydzik-
sp. Kwiatkowska and
Zielińska (2016)
Candidatus kuenenia and Excess ammonium was Park et al. (2014)
Nitrosomonas sp. eliminated from waterbodies
exhibiting high concentrations
Accumulibacter sp., Tetrasphaera Phosphorus contamination was Kong et al. (2007),
sp. and Dechloromonas sp. reduced from polluted aquatic Oehmen et al. (2007),
environments Nielsen et al. (2010),
Nguyen et al. (2011)
Sphingomonas bisphenolicum, Micropollutants of aquatic Mangwani et al. (2014),
pseudomonas paucimobilis, bodies, such as polycyclic Cydzik-Kwiatkowska
Sphingomonas sp. AO1 and P. aromatic hydrocarbon (PAH) and and Zielińska (2016)
mendocina NR802 bisphenol A, had undergone
biodegradation
Geobacter metallireducens and Effective bioremediation of heavy
Singh and Cameotra
pseudomonas putida metal contaminated water bodies(2004)
Fusarium sp., Graphium sp., Removal of chemicals like phenol
Santos and Linardi
Candida tropicalis, and and m-cresol from wastewater (2004), Ying et al.
Acinetobacter sp. (2007)
Bacillus cereus AUMC B52 and Acts as cost-effective bio-sorbent Joo et al. (2010)
P. aeruginosa ASU 6a material for the elimination of Zn
(II) from wastewater
Pseudomonas maltophilia, Plays a significant part in the Tsuruta (2004)
Acinetobacter calcoaceticus, P. bio-sorption of metals like gold
aeruginosa and Erwinia herbicola (au)
(continued)
4 Role of Modern Biotechnology in the Era of River Water Pollution 71
Table 4.4 (continued)
Biofilm-derived microbial isolates Environmental Benefits References
Escherichia coli Potential bioremediation agent Kao et al. (2006)
for several heavy metals, such as
cadmium (cd), lead (Pb), zinc
(Zn), and copper (cu)
Sphingomonas sp. and Effective against specific toxic Abou-Zeid et al. (2004),
Sphingpoyxis sp. compounds like aliphatic- Wu et al. (2010)
aromatic copolyesters,
microcystin-RR, and aliphatic
homopolyesters
Trichoderma sp., A. niger and Decreases dye contamination of Tatarko and Bumpus
basidiomycetes water (Congo red, Orange G.) by (1998), Sivasamy and
biosorption Sundarabal (2011)
Fig. 4.2 Schematic representation of removal of pollutants from an aquatic ecosystem (Wu
et al. 2012)
remove toxins from contaminated water. Figure 4.2 depicts the whole process of
removing toxins from the aquatic environment (Wu et al. 2012).
6 R
emoval of Pesticide from Polluted Water through
Remediation Technology
activity, high pollutant absorption rate, high growth rate, and easy harvesting, which
is being used in water treatment (Syuhaida et al. 2014).
According to Chuluun et al. (2009), Organophosphate (malathion, parathion,
diazinon, and fenitrothion) and Organochlorine (dieldrin, HCB) pesticides can be
absorbed from the aquatic ecosystems by A. Gramineus (Chuluun et al. 2009). The
potential of Atrazine removal of Lemna gibba and Azolla caroliniana has also been
reported by (Guimarães et al. 2011). Macrophyte species S. polyrhiza and L. minor
exhibited the highest rate of removal efficacy for the two particular fungicides, pyri-
methanil, and dimethomorph (Dosnon-Olette et al. 2009).
7 F
loating Treatment Wetlands as a Remediation Agent
of Contaminated Water
A novel technology that offers great potential for the treatment of polluted aquatic
ecosystems is Floating islands in Wetlands (Ladislas et al. 2015). Emergent wetland
plants developing hydroponically on structures form floating treatment wetlands
74 A. K. Rout et al.
Fig. 4.4 Schematic representation of a floating treatment wetland (modified version of Samal
et al. 2019)
(FTWs) (Fig. 4.4). The floating islands provide essential nutrients to the microbial
community, whose metabolic by-products are utilized as resources for other organ-
isms forming a complex network in a wetland (Chaudhuri et al. 2014). A large sur-
face area developed by the plant roots enhances the capacity for adsorption, biofilm
attachment, and storage of nutrients (Tanner and Headley 2011). FTWs are able to
withstand profound and fluctuating water levels when they expand through the
floating mat and into the water below. This approach can be regarded as a cost-
effective alternative along with ecological benefits.
8 Conclusion
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