MICROBIAL ENRICHMENT IN GLOBAL WASTEWATER NICHES UNDER IMPACT OF CLIMATE CHANGE - A COMPUTATIONAL STUDY 0120887828, 9781118960608

Table of contents :
Article_12

Citation preview

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022

Print : ISSN : 0973-0834

Received : 12 November, 2022 / Reviewed & Accepted : 12 December, 2022 / Uploaded Online : June, 2023

MICROBIAL ENRICHMENT IN GLOBAL WASTEWATER NICHES UNDER IMPACT OF CLIMATE CHANGE - A COMPUTATIONAL STUDY Souptik Ghosh1*, Nabarun Dawn1*, Souradip Basu2 and Sayak Ganguli1# Graduate Department of Biotechnology, St. Xavier’s College (Autonomous); Kolkata 2Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous); Kolkata Email: [email protected],[email protected], [email protected] *Equal Contribution; # Corresponding author: [email protected] 1Post

ABSTRACT With rise in industrialization and human activities, global warming and eventually climate change concerns are looming large on the face of humankind. Wastewater, being the sink for local microbial community can be assessed and analyzed as an indicator for climate change. Impacts of global warming are far-reaching and cause changes in life processes occurring in Nature, which gets reflected on the abundance of microorganisms detected in the wastewater. Greenhouse gases like Methane and Nitrous oxide, are the major players of global warming. The data used in our research was collected from rural, urban and delta region of India, regions of São Paulo, Brazil, along with domestic and industrial regions of Henan, China. The data were analyzed after thorough metagenomics study. Changes in nutrient cycling, such as carbon and nitrogen cycling, rise of several diseases and antibiotic resistance amongst the microorganisms have been detected. Increase in mean temperature of earth will also cause changes in the life processes of microorganisms and the ones which can survive outside the temperature niche of initial habitat can survive. Thus, by observing these six data sets, we aim to investigate the roles of microbes present in wastewater as an indicator for climate change. Key words: Climate Change, Wastewater, Global warming, Methane, Nitrous oxide

221

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. INTRODUCTION Climate change and Global Warming is a significant challenge in this era. It disrupts species’ interactions causing the species to either adapt or perish. Microorganisms are present on Earth’s surface from time immemorial (Knauth, 2005) and hence, have undergone the longest periods of evolution by acquiring characteristics to withstand extreme stresses (Konhauser et al., 2003). Earth’s mean temperature is expected to rise by 1.5°C beyond pre-industrial level (IPCC, 2022). With temperature, precipitation patterns alter (Easterling et al., 2000), impacting majorly on carbon cycle (Cox et al., 2000). Soil respiration is a principal carbon exchange pathway between terrestrial ecosystems and atmosphere, which if altered will heavily impact on carbon cycling, ecosystem feedback and responses, and subsequently, cause climate change (Luo and Zhou, 2006). Niche is the part or position of a particular species in a community and its distributional relation based on different environments (Pulliam, 2000). Its ecosystem functioning is majorly reliant on two factors: (i) its structure (Osorio-Olvera et al., 2019) and (ii) microbial community organization (Larkin & Martiny, 2017). Microbes play the role of producers and consumers of Greenhouse Gases (GHGs) by participating in biogeochemical cycles and maintain a balance using feedback responses. GHGs include Nitrous Oxide (N2O), Methane (CH4), Chlorofluorocarbons (CFCs), Carbon dioxide (CO2), and Ozone (O3). They act as a greenhouse by allowing solar heat to penetrate through atmosphere, but blanketing it from returning into space, thus increasing Earth’s surface temperature. Temperature is important in maintaining a balance between carbon consumption and emission. Microbes can mitigate negative influences of climate change due to their versatility in growth and metabolism. Soil runoffs and wastewater containing microbial load, are discharged into drainage system which acts as a microbial sink (Lara-Martín et al., 2020). Microbial bioremediation of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), pesticides, metals, etc. can reduce water pollution. During stresses, they allot more organicresources to survival pathways, than to growth pathways. Dormancy and cell death are induced for intolerable stresses, causing removal of microbial function (Suzina et al., 2004) and considerable delays in regaining back activity when favorable conditions return (Clein et al., n.d.). As microorganisms die, nutrients like amino acids, inorganic phosphates, etc., are released which can be absorbed by plants or other microbes, for survival, cryptic growth, (Chapman et al., n.d.) or for performing denitrification (Sharma et al., 2006). However, all microbes aren’t beneficial and climate change has aggravated emergence of new diseases due to increased growth and metabolism at increased temperatures. The biggest drawback of climate change is that it may increase AntiMicrobial Resistance (AMR) rate amongstpathogens. A 10°C rise in temperature can increase AMR by up to 4-10%. Mobile resistance genes can undergo horizontal gene transfer (HGT) at increased temperatures, increasing the rate of pathogen growth and transmission (MacFadden et al., 2018). This will in turn increaseantibiotic 222

Microbial enrichment in global wastewater niches under impact of climate.... usageandresult in more bacteria showing AMR (Cabello et al., 2016). Thus, wastewater microbial analysis is a good indicator for local mean temperature and climate change. Table 1. Showing datasets used in current research Abbreviations IR IU ID SP HD HI

Wastewater samples collected from Rural area, India (Set-1) Urban area, India (Set-2) Sundarbans Delta area, India (Set-3) São Paulo, Brazil (Set-4) Henan, China (Domestic) (Set-5) Henan, China (Industrial) (Set-6)

MATERIAL AND METHODS Four web servers were used for our analysis. They are as follows: 1. MetaG: https://www.bioinformatics.uni-muenster.de/tools/metag/index.hbi MetaG is used to obtain data regarding taxonomic assignment from individual reads to whole sample. Reads are supplemented with run-time and parameter data (Wattam et al., 2017). 2. Venny 2.1.0: https://bioinfogp.cnb.csic.es/tools/venny/ This server takes in lists of 2,3,4 datasets to find common elements between them using Venn diagrams. The overlapped regions show common relationships whereas the non-overlapped region show the unique data in the lists. 3. iVikodak Global Mapper: https://web.rniapps.net/iVikodak/global.php iVikodak Global Mapper uses 16S microbiome datasets to suggest microbial environments’ functional profiles (Markowitz et al., 2012). The functions can be performed by the server are Top functions, Core functions, Differentiating functions, Ordination Analysis and Function driven Correlation networks. 4. Microbiome Analyst- Taxon Set Enrichment Analysis (TSEA): https://dev. microbiomeanalyst.ca/MicrobiomeAnalyst/upload/TaxaUpload.xhtml This server is designed to check presence of patterns of biological and ecological importance using user-submitted taxa (Ma et al., 2017). Findings are represented as an interactive network which gives significant taxon set inter-relationships and a table of results is present at the bottom (Merico et al., 2010). A node with a colour intensity based on its P value and size based on number of hits, represents one single taxon set. Taxon sets are linked if their shared hits are >20% of their entire taxa’s sum. RESULTS AND DISCUSSION Fastq files of 6 sets were uploaded into MetaG server setting database as RDP_16S_28S and database profile as Illumina. The details of each dataset andthe abundance of genera have been represented as a Krona chart. 223

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. IR consisted of 45536 bacterial and 5137 archaeal reads, of which Methanothrix (17.3%) and Smithella (9.9%) were most abundant.

Fig. 1. IR-Summary graph

IU consisted of 48471 bacterial and 52 archaeal reads, of which Sulfurospirillum (24.7%) and Cloacibacterium (8.1%) were most abundant.

Fig. 2. IU-Summary graph.

224

Microbial enrichment in global wastewater niches under impact of climate.... ID consisted of 140071 bacterial and 38 archaeal reads, of which Pseudoalteromonas (49.9%) and Bacillariophyta (10.9%) were most abundant.

Fig. 3. ID-Summary graph.

SP consisted of 181260 bacterial and 83 archaeal reads, of which Lactobacillus (49.9%) were most abundant.

Fig. 4. SP-Summary graph.

225

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. HD consisted of 51941 bacterial reads, of which Aridibacter (16.1%) and Hyphomicrobium (8.4%) were most abundant.

Fig. 5. HD -Summary graph.

HI consisted of 45642 bacterial reads, of which Meiothermus (34.7%) and Hyphomicrobium (15.4%) were most abundant.

Fig. 6. HI -Summary graph.

Common genera were obtained using Venny 2.1.0, one between Indian samples namely, IR, IU and ID; and the other between foreign samples namely, SP, HD and HI. For Indian samples, 19 (6.4%) are common between them, which are Geobacter, Prevotella, Clostridium sensu stricto, Streptococcus, Escherichia, Propionibacterium, 226

Microbial enrichment in global wastewater niches under impact of climate.... Lactobacillus, Thauera, Acidovorax, Novosphingobium, Burkholderia, Pseudomonas, Sphingomonas, Cloacibacterium, Acinetobacter, Corynebacterium, Rhizobium, Staphylococcus and Rothia. In case of foreign samples, 9 (4.8%) are common between them, which are Thauera, Rhizobium, Diaphorobacter, Hyphomicrobium, Gp3, Pseudomonas, Nitrosomonas, Gemmatimonas and Acidovorax.

Fig. 7. Venn diagrams representing common genera between Indian samples (on left) and foreign samples (on right)

Using the common genera, a heatmap was generated using iVikodak Global mapper (Figures 9-10) to predict the core functions, for Indian and foreign samples.

Fig. 8. Heatmap representing the core functions of IR, IU, and ID, respectively.

Fig. 9. Heatmap representing the core functions of SP, HD, and HI, respectively.

227

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. Several core functions were predicted of varying likelihood of enrichments, some of which are studied in Table 2. Table 2. Likelihood of core function enrichment in all the samples, where 0 and 1 are the minimum and maximum chances of enrichment, respectively. Likelihood of enrichment

Core functions

IR

IU

ID

SP

HD

HI

Beta-lactam resistance

0.5

0

1

0.5

1

0

Vancomycin resistance

0.5

0

1

1

0.5

0

Sulfur metabolism

0.5

0

1

0.5

1

0

Nitrogen metabolism

0.5

0

1

1

0.5

0

Methane metabolism

0.5

0

1

0

0.5

1

Carbon fixation pathways in prokaryotes

0.5

0

1

0.5

1

0

0

0.5

1

1

0.5

0

Benzoate degradation

Function-driven hierarchical microbial network analysis for the microbiome pertaining to Indian and foreign samples were obtained, showing the presence of bi-directional (as red lines) and uni-directional (as blue lines) interactions (Fig. 10).

Fig. 10. Network analysis of (A) Indian samples and (B) foreign samples.

Using Microbiome Analyst, Mixed level Taxon Set Enrichment Analysis was performed using parameter “Host-intrinsic taxon sets”. Enrichment network of nodes (shown in Figures 12-16) and a detailed result table were obtained. No network was obtained for HI. Table 3 shows a summary of major diseases, and their underlying taxon sets responsible. 228

Microbial enrichment in global wastewater niches under impact of climate....

Fig. 11. Set-1: Interactive Disease Network.

Fig. 12. Set-2: Interactive Disease Network.

229

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al.

Fig. 13. Set-3: Interactive Disease Network.

Fig. 14. Set-4: Interactive Disease Network.

230

Microbial enrichment in global wastewater niches under impact of climate....

Fig. 15. Set-5: Interactive Disease Network.

Table 3. Summary of major diseases caused by microbial genera. SL. No.

Diseases

Associated Genera

1

Alzheimer’s

Bacteroides; Alistipes; Phascolarctobacterium; Gemella; Blautia;

2

Bacterial Vaginosis

Leptotrichia; Lactobacillus; Megasphaera; Olsenella; Prevotella;

3

Chronic Obstructive Haemophilus; Prevotella; Pseudomonas; Burkholderia; Pulmonary Disease (COPD) Lactobacillus;

4

Cirrhosis (China)

Streptococcus; Prevotella; Lactobacillus; Fusobacterium; Megasphaera; Haemophilus;

5

Colorectal cancer

Fusobacterium; Porphyromonas; Prevotella; Dialister; Peptostreptococcus; Gemella;

6

HPV

Brevibacterium; Pseudomonas; Pediococcus;

7

Maternal Antenatal infection

Arthrobacter; Klebsiella; Acinetobacter; Streptococcus; Pseudoalteromonas;

8

Pediatric Crohn’s Disease

Bacteroides; Faecalibacterium; Blautia; Ruminococcus;

9

Type-I Diabetes

Granulicatella; Ruminococcus; Alistipes; Enterobacter; Escherichia; Lactobacillus; Streptococcus;

10 Urogenital schistosomiasis

Megasphaera; Dialister; Acinetobacter; Prevotella; Desulfovibrio; Olsenella; Haemophilus;

231

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. With rise in temperatures due to GHGaccumulation, microbial community composition is changed and replaced by microbiota which can tolerate those temperatures and thrive by increased microbial decomposition, fermentation, respiration and methanogenesis (E et al., 2018). These factors positively correlate with global warming and increase GHG emission. High abundance of methanogens and methanotrophs, which produce and consume methane respectively, are seen especially in IR, with methanogens being Methanobacterium, Methanobrevibacter, Methanocorpusculum, Methanolinea, Methanosarcina, Methanospirillum and Methanothrix and methylotrophs being Methylocystis, Methylosarcina, Methylotenera, Methyloversatilis. Hyphomicrobium, a methylotroph is present in huge numbers in both the Chinese HI and HD, but not reported in Indian samples, indicating a spatial-temporal role. Together, they maintain a healthy methane balance (Bousquet et al., 2006). The methane cycle pathway is shown in Fig. 17. High incidence in IR may be due to better plant cover in rural areas which augment and regulate this cycle (Kollah et al., 2018). Methanosarcina has been observed to degrade CFC-11 by anoxic reductive dehalogenation (Krone and Thauer, 1992). Methanogens can abiotically degrade rapidly CFC-113 as reported (Lesage et al., 1992) in a landfill leachate. Organohalide-respiring bacteria (OHRB) derive energy from aromatic and/or aliphatic halogenated compounds dehalogenation and reduce their hazardous contamination with groundwater (Jackson, 2004). Geobacter, Desulfuromonas, Anaeromyxobacter, Desulfomonile, and Dehalococcoides found in IR and, Sulfurospirillum and Desulfovibrio found in huge numbers in IU are some of the OHRB found in our research (Hug et al., 2013). Carbon cycle and CO2 release are regulated by atmospheric carbonfixing microbes, by decomposing dead organic material (Crowther et al., 2015). Chemotrophs use inorganicand organic carbon substrates for their own metabolism and energy source, and lower CO2 release and global warming. Bacteria and archaea Fig. 16. Methane cycle involved in wastewater. can convert CO2 to vital sugars. With every 5-10°C rise in temperature, microbial respiration and activity in degrading carbon-based materials increases and more CO2 is emitted (E et al., 2018). With more CO2, global warming rises and in turn, speeds up microbial activity like a 232

Microbial enrichment in global wastewater niches under impact of climate.... vicious cycle. Under anaerobic conditions, microbes produce energy by fermenting carbon compounds. Thiobacillus gets energy from an electron removal Fe-containing compounds to convert carbon. Bacteroides, Clostridium, and Syntrophomonas (found majorly in IR and IU) can collaborate to degrade anaerobically carbon (E et al., 2018). Smithella and Syntrophomonas present in IR imply a multi-trophic interaction between them to produce acetate and butyrate from propionate, and acetate from butyrate, respectively (Puengrang et al., 2020). Paludibacter found in IR and IU is a propionate and acetate-producing bacterium through fermentation (Qiu et al., 2014). Sulfate-reducing bacteria can use sulfate, hydrogen, and different organic and inorganic compounds to respire anaerobically and thrive in environments with wide extremes of pH, temperature, and salinity conditions. They are involved in cycles of carbon and sulfur and play a beneficial role in removing heavy metals and sulfur oxides from the environment. They interact metabolically with methanogens by competing for acetate and hydrogen, in presence of sulfate. In sulfate’s absence, they thrive syntrophically with methanogens. Our dataset shows the presence of sulfate-reducing bacteria like Fig. 17. Sulfur cycle by sulfate-reducing bacteria and Desulfatiglans, Desulfobulbus, its associated methane metabolism. Desulforhabdus, Desulfovibrio, Desulfurivibrio, and Desulfuromonas,especially in IR, and their co-presence with methanogens and methylotrophs implies a possible inter-relationship between carbon, methane, and sulfur cycles in IR wastewater (Muyzer and Stams, 2008). Fig. 17 shows the sulfur cycle. N2O is the most potent GHG. From natural sources, it is emitted from nitrogen cycling by both nitrification and denitrification, contributing about 70% to N2O budget globally (Butterbach-Bahl et al., 2013). Both nitrifying bacteria and methanotrophs produce N2O during nitrification when the pO2 is between 0.1–0.5 kPa. Under strict anaerobic conditions, it is also produced by denitrifying bacteria (Kollah et al., 2018). Climate change disrupts the rate of nitrogen cycling processes and releasing of N2O. N2O production bynitrogen cycleby microbes found from our research are detailed in Fig. 18. Rhizobium is found fairly in all the samples, suggesting its role in symbiotic 233

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. nitrogen fixation (Vitousek et al., 2013). Nitrosomonas and Nitrospira, mostly present in HD and HI, are litho-autotrophic bacteria which oxidize ammonia as sole energy source to nitrites and nitrates by nitrification, and using the CalvinBenson cycle, fix CO2 (Kollah et al., 2018). Other microbes involved in nitrogen cycle are denitrifying bacteria like Acidovorax, Clostridium, Diaphorobacter, Pseudomonas, Rothia, Aridibacter and Thauera (Chen et al., 2019; Gtari et al., 2012; Scholten et al., 1999; Yang et al., 2013; Z-d et al., 2021). Acidovorax, an acetate-utilizing denitrifier (Ginige et al., 2005), is seen in every sample. They are aerobic, chemoorganotrophs, although some strains can anaerobically grow using NO3- as terminal electron acceptor (Willems and Gillis, 2015). Diaphorobacter is a Poly (3-hydroxybutyrate-coFig. 18. N2O production from nitrogen cycle. 3-hydroxyvalerate)-degrading denitrifying bacteria, mostly present in UI and HI (Khan and Hiraishi, 2002). Some denitrifying bacteria can consume N2O and mitigate emissions (Charu Gupta et al., 2014). Under denitrifying conditions, Bacillus, Staphylococcus, Streptococcus, Dechloromonas, Thauera, and Zoogloea can breakdown aromatic hydrocarbons (Joutey et al., 2013; Kouzuma and Watanabe, 2011; Mao et al., 2010; Zhang et al., 2021). Additionally, Thaueracan tolerate saline, alkaline, and high temperature environments, indicating their presence in all the samples (Pal et al., 2018). Novosphingobium, Sphingomonas, Sulfuricurvum, Telmatospirillum and Pseudoalteromonas can degrade PAHs (de Mandal et al., 2019; Hedlund and Staley, 2006; Sohn et al., 2004). Acinetobacter and Pseudomonas found in all the samples, can degrade phenol, benzoate and fluorobenzene, reduce toxicity by converting Cr (VI) to Cr (III), and remove Fe and Mn (Li et al., 2016; Nancharaiah et al., 2010; Ojha et al., 2021). Burkholderia uses 2,3,4,5,6-pentafluorobiphenyl and 4,4´-difluorobiphenyl as its carbon and energy source. It can degrade 2,4-dichlorophenoxyacetic acid (2,4-D), and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) (Huong et al., 2007; Yousra Turki et al., 2017). Other PCB-degrading bacteria are Ralstonia, Achromobacter, and Comamonas, mostly found in HI (Joutey et al., 2013). Povalibacter found in HD and HI can 234

Microbial enrichment in global wastewater niches under impact of climate.... degrade Polyvinyl alcohols (Nogi et al., 2014). The abundance of these microbes provide evidence that complex hydrocarbons are present in wastewater, which can be biologically degraded by them. Some moderately thermophilic microorganisms have been found, namely Syntrophothermus, Thermoanaerobaculum, Thermodesulfobium, Thermogutta, Thermomonas and Meiothermus, implying that 45-60°C temperatures exist in these areas. Hot untreated industrial wastewater and rising mean temperatures are the main reasons for their growth augmentation (Al-Daghistani et al., 2021; Losey et al., 2013; Mori and Hanada, 2015; Sekiguchi et al., 2000; Slobodkina et al., 2015). Hospital wastewater contains diverse range of Antibiotic Resistance Genes (ARGs), which can be a potential health hazard. Acinetobacter, Burkholderia, Corynebacterium, Escherichia, Staphylocococcus, Streptococcus and Pseudomonas,present in significant amounts, can either acquire ARGs for encoding β-Lactamase, which cleaves the antibiotic β-lactam ring (Bush and Jacoby, 2010), or they can efflux out antibiotics before theirarrival at the target site to produce the desired effect or undergo mutations to downregulate porin genes, which can either restrict access to antibiotic binding sites on cell wall or can acquire genes which changes metabolic pathway and alter the antibiotic binding site (Tenover, 2006). Indiscriminate antibiotic usage along with pollution and climate change are giving rise to drug resistant Vibrio sp. as reported in Indian aquaculture farms (Devi et al., 2009). Extensive antibiotic usage, pollution by biocides and heavy metals, and climate change regulates HGT (Mizuno & Mizushima, 1990). Climate change affects plasmid replicationand increases HGT-related enzyme activity (Tamang et al., 2017). In Vibrio harveyi, transfer of SXT (Hochhut et al., 2001), an Integrative and Conjugative Element (ICE) (Burrus & Waldor, 2004), in presence of ciprofloxacin confers trimethoprim, streptomycin, sulfamethoxazole, and chloramphenicol resistance (Beaber et al., n.d.). Shiga Toxin (STX) prophage induction and STX phage-mediated gene transfer rise in high temperatures with UV irradiation (Tamang et al., 2017). To conclude, human practices andpollution have disrupted microbial community structure and function, causing alteredcarbon and nitrogen cycling. Water surface temperature has risen, facilitating opportunistic microbial respiration and fermentation, producing CO2. Consequently, many vector-borne diseases have emerged. Microbes act as both the source and the sink for GHGs. Introducing genes that can metabolize GHGs can reduce microbial GHG emission. Current agricultural practices need modifications to reduce CH4 and N2O emission. Biofertilizers instead of synthetic nitrogen fertilizers, and denitrifying bacteria that convert N2O into atmospheric N2, can mitigate N2O emission. CH4 uses soil as a sink. High-affinity Methane Oxidation (HAMO) by methanotrophsto mitigate its emission can be enhanced by alternately wetting-drying and draining soil. Hospital wastewater should be treated before discharging. 235

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. ACKNOWLEDGEMENTS The authors would like to thank Reverend Father Principal of St. Xavier’s College, Kolkata, Dr. Dominic Savio, S.J. Dr. Jhimli Dasgupta, HOD, Department of Biotechnology and all the faculties of the department for the necessary encouragement and permissions. CONFLICT OF INTEREST: The authors declare that the manuscript is original and no parts of it has been published previously. They also declare that they do not have any conflict of interest. REFERENCES Abatenh, E., Gizaw, B., Tsegaye, Z. and Genene, T. 2018. Microbial Function on Climate Change – A Review. Open Journal of Environmental Biology., 001007. https://doi.org/10.17352/OJEB.000008 Al-Daghistani, H. I., Mohammad, B. T., Kurniawan, T. A., Singh, D., Rabadi, A. D., Xue, W., Avtar, R., Othman, M. H. D. and Shirazian, S. 2021. Characterization and applications of Thermomonas hydrothermalis isolated from Jordan’s hot springs for biotechnological and medical purposes. Process Biochemistry., 104, 171–181. https://doi.org/10.1016/J.PROCBIO.2021.03.010 Beaber, J., Hochhut, B., Nature, M. W. and undefined. (n.d.). 2004. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature.Com.. Retrieved August 3, 2022, from https://idp.nature.com/authorize/casa?redirect_ uri=https://www.nature.com/articles/nature02241&casa_token=iKHiLv00hCw AAAAA:urXLr8SfSq0jAZYnnI9_Q0czs6OxfHo1FsCSJnJd-w93EUW4-qW1Pfnf_ g7J2epBFs8pcGNMUEGWMDqObA Bousquet, P., Ciais, P., Miller, J. B., Dlugokencky, E. J., Hauglustaine, D. A., Prigent, C., van der Werf, G. R., Peylin, P., Brunke, E. G., Carouge, C., Langenfelds, R. L., Lathière, J., Papa, F., Ramonet, M., Schmidt, M., Steele, L. P., Tyler, S. C. and White, J. 2006. Contribution of anthropogenic and natural sources to atmospheric methane variability. Nature., 443(7110): 439-443. https://doi. org/10.1038/NATURE05132 Burrus, V. and Waldor, M. K.2004. Shaping bacterial genomes with integrative and conjugative elements. Research in Microbiology., 155(5): 376-386. https://doi. org/10.1016/j.resmic.2004.01.012 Bush,

K. and Jacoby, G. A. 2010. Updated functional classification of β-lactamases. Antimicrobial Agents and Chemotherapy., 54(3), 969–976. https://doi.org/10.1128/AAC.01009-09/ASSET/7642BBDF-C04B-44A4-931177D570253BF5/ASSETS/GRAPHIC/ZAC9991087260003.JPEG 236

Microbial enrichment in global wastewater niches under impact of climate.... Butterbach-Bahl, K., Baggs, E. M., Dannenmann, M., Kiese, R. and ZechmeisterBoltenstern, S. 2013. Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Philosophical Transactions of the Royal Society B: Biological Sciences., 368(1621). https://doi.org/10.1098/ RSTB.2013.0122 Cabello, F. C., Godfrey, H. P., Buschmann, A. H. and Dölz, H. J. 2016. Aquacultureas yet another environmental gateway to the development and globalisation of antimicrobial resistance. Lancet Infect. Dis., 16(7), e127–e133. https://doi. org/10.1016/S1473-3099(16)00100-6 Chapman, S., biochemistry, T. G.-S. biology and undefined. (n.d.). 1986. Importance of cryptic growth, yield factors and maintenance energy in models of microbial growth in soil. Elsevier. Retrieved August 1, 2022, from https://www. sciencedirect.com/science/article/pii/0038071786900957 Chen, S., Perathoner, S., Ampelli, C. and Centi, G. 2019. Electrochemical Dinitrogen Activation: To Find a Sustainable Way to Produce Ammonia. Studies in Surface Science and Catalysis., 178: 31-46. https://doi.org/10.1016/B978-0-444-641274.00002-1 Clein, J. and Biochemistry, J. S. -S. B. 1994, undefined. (n.d.). Reduction in microbial activity in Birch litter due to drying and rewetting event. Elsevier., Retrieved August 1, 2022, from https://www.sciencedirect.com/science/article/ pii/0038071794902909 Cox, P. M., Betts, R. A., Jones, C. D., Spall, S. A. and Totterdell, I. J. (2000). Acceleration of global warming due to carbon-cycle feedbacks in a coupled climate model. Nature., 408(6809): 184-187. https://doi.org/10.1038/35041539 Crowther, T. W., Thomas, S. M., Maynard, D. S., Baldrian, P., Covey, K., Frey, S. D., van Diepen, L. T. A. and Bradford, M. A. (2015). Biotic interactions mediate soil microbial feedbacks to climate change. Proceedings of the National Academy of Sciences of the United States of America., 112(22): 7033-7038. https://doi. org/10.1073/PNAS.1502956112/SUPPL_FILE/PNAS.201502956SI.PDF De Mandal, S., Mathipi, V., Muthukumaran, R. B., Gurusubramanian, G., Lalnunmawii, E. and Kumar, N. S. 2019. Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes. Environmental Monitoring and Assessment, 191(12), 1-13. https://doi.org/10.1007/S10661-0197879-0/FIGURES/7 Devi, R., Surendran, P. K. and Chakraborty, K. (2009). Antibiotic resistance and plasmid profiling of Vibrio parahaemolyticus isolated from shrimp farms along the Southwest coast of India. World Journal of Microbiology and Biotechnology., 25(11): 2005-2012. https://doi.org/10.1007/S11274-009-0101-8 237

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. Easterling, D. R., Meehl, G. A., Parmesan, C., Changnon, S. A., Karl, T. R. and Mearns, L. O. (2000). Climate extremes: Observations, modeling, and impacts. Science., 289(5487): 2068-2074. https://doi.org/10.1126/SCIENCE.289.5487.2068 Ginige, M. P., Keller, J. and Blackall, L. L. 2005. Investigation of an acetatefed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography. Applied and Environmental Microbiology., 71(12): 8683-8691. https://doi. org/10.1128/AEM.71.12.8683-8691.2005/ASSET/B45534A9-CF2B-42A7-A107AEFE1C0451BC/ASSETS/GRAPHIC/ZAM0120561020003.JPEG Gtari, M., Ghodhbane-Gtari, F., Nouioui, I., Beauchemin, N. and Tisa, L. S. 2012. Phylogenetic perspectives of nitrogen-fixing actinobacteria. Archives of Microbiology., 194(1): 3-11. https://doi.org/10.1007/S00203-011-0733-6 Gupta, C., Prakash, D. and Gupta., S. 2014. Role of microbes in combating global warming Int. J. Pharm. Sci., 4: 359-363. Hedlund, B. P. and Staley, J. T. 2006. Isolation and characterization of Pseudoalteromonas strains with divergent polycyclic aromatic hydrocarbon catabolic properties. Environmental Microbiology, 8(1): 178-182. https://doi. org/10.1111/J.1462-2920.2005.00871.X Hochhut, B., Lotfi, Y., Mazel, D., Faruque, S. M., Woodgate, R. and Waldor, M. K. 2001. Molecular Analysis of Antibiotic Resistance Gene Clusters in Vibrio cholerae O139 and O1 SXT Constins. Antimicrobial Agents and Chemotherapy, 45(11), 2991-3000. https://doi.org/10.1128/AAC.45.11.2991-3000.2001 Hug, L. A., Maphosa, F., Leys, D., Löffler, F. E., Smidt, H., Edwards, E. A., and Adrian, L. 2013. Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philosophical Transactions of the Royal Society B: Biological Sciences., 368(1616). https://doi.org/10.1098/ RSTB.2012.0322 Huong, N. L., Itoh, K. and Suyama, K. 2007. Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacteria in Vietnamese Soils. Microbes and Environments., 22(3): 243-256. https://doi. org/10.1264/JSME2.22.243 IPCC. 2022. Global Warming of 1.5°C. Global Warming of 1.5°C. https://doi. org/10.1017/9781009157940 Jackson, R. E. 2004. Recognizing Emerging Environmental Problems: The Case of Chlorinated Solvents in Groundwater. Technology and Culture., 45(1): 55-79. https://doi.org/10.1353/TECH.2004.0022 Joutey, N. T., Bahafid, W., Sayel, H. and El Ghachtouli, N. 2013. Biodegradation: Involved Microorganisms and Genetically Engineered Microorganisms. Biodegradation - Life of Science. https://doi.org/10.5772/56194 238

Microbial enrichment in global wastewater niches under impact of climate.... Khan, S. T. and Hiraishi, A. 2002. Diaphorobacter nitroreducens gen nov, sp nov, a poly (3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge. The Journal of General and Applied Microbiology, 48(6): 299-308. https://doi.org/10.2323/JGAM.48.299 Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. and Frith, M. C. 2011. Adaptive seeds tame genomic sequence comparison. Genome Research, 21(3): 487-493. https:// doi.org/10.1101/gr.113985.110 Knauth, L. P. 2005. Temperature and salinity history of the Precambrian ocean: implications for the course of microbial evolution. In Geobiology: Objectives, Concepts, Perspectives (pp. 53-69). Elsevier. https://doi.org/10.1016/B978-0-44452019-7.50007-3 Kollah, B., Patra, A. K. and Mohanty, S. R. 2018. Microbial Cycling of Greenhouse Gases and Their Impact on Climate Change. 129-143. https://doi.org/10.1007/978981-10-6178-3_7 Konhauser, K. O., Jones, B., Reysenbach, A. L. and Renaut, R. W. 2003. Hot spring sinters: keys to understanding Earth’s earliest life forms. Canadian Journal of Earth Sciences, 40(11): 1713-1724. https://doi.org/10.1139/E03-059 Kouzuma, A. and Watanabe, K. 2011. Molecular Approaches for the Analysis of Natural Attenuation and Bioremediation. Comprehensive Biotechnology, Second Edition, 6: 25-36. https://doi.org/10.1016/B978-0-08-088504-9.00375-5 Krone, U. E. and Thauer, R. K. 1992. Dehalogenation of trichlorofluoromethane (CFC-11) by Methanosarcinabarkeri. FEMS Microbiology Letters, 69(2): 201204. https://doi.org/10.1016/0378-1097(92)90629-3 Lara-Martín, P. A., Chiaia-Hernández, A. C., Biel-Maeso, M., Baena-Nogueras, R. M. and Hollender, J. 2020. Tracing Urban Wastewater Contaminants into the Atlantic Ocean by Nontarget Screening. Environmental Science and Technology, 54(7): 3996-4005. https://doi.org/10.1021/acs.est.9b06114 Larkin, A. A. and Martiny, A. C. 2017. Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. Environmental Microbiology Reports, 9(2), 55-70. https://doi.org/10.1111/1758-2229.12523 Lesage, S., Brown, S. and Hosler, K. R. 1992. Degradation of chlorofluorocarbon-113 under anaerobic conditions. Chemosphere, 24(9): 1225-1243. https://doi.org/ 10.1016/0045-6535(92)90049-W Li, C., Wang, S., Du, X., Cheng, X., Fu, M., Hou, N. and Li, D. 2016. Immobilization of iron- and manganese-oxidizing bacteria with a biofilm-forming bacterium for the effective removal of iron and manganese from groundwater. Bioresource Technology, 220: 76-84. https://doi.org/10.1016/J.BIORTECH.2016.08.020

239

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. Losey, N. A., Stevenson, B. S., Busse, H. J., Damsté, J. S. S., Rijpstra, W. I. C., Rudd, S. and Lawson, P. A. 2013. Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring. International Journal of Systematic and Evolutionary Microbiology, 63(Pt 11): 4149-4157. https://doi.org/10.1099/IJS.0.051425-0 Luo, Y. and Zhou, X. 2006. Soil Respiration and the Environment. Soil Respiration and the Environment. https://doi.org/10.1016/B978-0-12-088782-8.X5000-1 Ma, W., Huang, C., Zhou, Y., Li, J. and Cui, Q. 2017. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes. Sci. Rep., 7: 1, 7(1), 1-6. https://doi.org/10.1038/srep40200 MacFadden, D. R., McGough, S. F., Fisman, D., Santillana, M. and Brownstein, J. S. 2018. Antibiotic resistance increases with local temperature. Nat. Clim., 8: 6, 8(6): 510-514. https://doi.org/10.1038/s41558-018-0161-6 Mao, Y., Zhang, X., Xia, X., Zhong, H. and Zhao, L. 2010. Versatile aromatic compounddegrading capacity and microdiversity of Thauera strains isolated from a coking wastewater treatment bioreactor. Journal of Industrial Microbiology and Biotechnology, 37(9): 927-934. https://doi.org/10.1007/S10295-010-0740-7 Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Jacob, B., Huang, J., Williams, P., Huntemann, M., Anderson, I., Mavromatis, K., Ivanova, N. N. and Kyrpides, N. C. 2012. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Research, 40(D1): D115-D122. https://doi.org/10.1093/nar/gkr1044 Merico, D., Isserlin, R., Stueker, O., Emili, A. and Bader, G. D. 2010. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation. PLOS ONE, 5(11): e13984. https://doi.org/10.1371/JOURNAL. PONE.0013984 Mizuno, T. and Mizushima, S. 1990. Signal transduction and gene regulation through the phosphorylation of two regulatory components: the molecular basis for the osmotic regulation of the porin genes. Molecular Microbiology, 4(7): 1077-1082. https://doi.org/10.1111/j.1365-2958.1990.tb00681.x Mori, K. and Hanada, S. 2015. Thermodesulfobium. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-5. https://doi.org/10.1002/9781118960608.GBM00753 Muyzer, G. and Stams, A. J. M. 2008. The ecology and biotechnology of sulphatereducing bacteria. Nature Reviews Microbiology., 6: 6, 6(6): 441-454. https:// doi.org/10.1038/nrmicro1892 Nagpal, S., Haque, M. M. and Mande, S. S. 2016. Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets. PLOS ONE, 11(2): e0148347. https://doi.org/10.1371/ journal.pone.0148347 240

Microbial enrichment in global wastewater niches under impact of climate.... Nancharaiah, Y. v., Dodge, C., Venugopalan, V. P., Narasimhan, S. v. and Francis, A. J. 2010. Immobilization of Cr(VI) and Its Reduction to Cr(III) Phosphate by Granular Biofilms Comprising a Mixture of Microbes. Applied and Environmental Microbiology, 76(8): 2433. https://doi.org/10.1128/AEM.02792-09 Nogi, Y., Yoshizumi, M., Hamana, K., Miyazaki, M. and Horikoshi, K. 2014. Povalibacteruvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes. International Journal of Systematic and Evolutionary Microbiology, 64(Pt 8): 2712-2717. https://doi.org/10.1099/IJS.0.062620-0 Ojha, N., Karn, R., Abbas, S. and Bhugra, S. 2021. Bioremediation of Industrial Wastewater: A Review. IOP Conference Series: Earth and Environmental Science, 796(1): 012012. https://doi.org/10.1088/1755-1315/796/1/012012 Osorio-Olvera, L., Soberón, J. and Falconi, M. 2019. On population abundance and niche structure. Ecography, 42(8): 1415-1425. https://doi.org/10.1111/ ECOG.04442 Pal, D., Bhardwaj, A., Sudan, S. K., Kaur, N., Kumari, M., Bisht, B., Vyas, B., Krishnamurthi, S. and Mayilraj, S. 2018. Thauerapropionica sp. nov., isolated from downstream sediment sample of the river ganges, Kanpur, India. International Journal of Systematic and Evolutionary Microbiology, 68(1): 341346. https://doi.org/10.1099/IJSEM.0.002508/CITE/REFWORKS Puengrang, P., Suraraksa, B., Prommeenate, P., Boonapatcharoen, N., Cheevadhanarak, S., Tanticharoen, M. and Kusonmano, K. 2020. Diverse Microbial Community Profiles of Propionate-Degrading Cultures Derived from Different Sludge Sources of Anaerobic Wastewater Treatment Plants. Microorganisms, 8(2). https://doi.org/10.3390/MICROORGANISMS8020277 Pulliam, H. R. 2000. On the relationship between niche and distribution. Ecology Letters, 3(4): 349-361. https://doi.org/10.1046/j.1461-0248.2000.00143.x Qiu, Y. L., Kuang, X. Z., Shi, X. S., Yuan, X. Z., and Guo, R. B. 2014. Paludibacterjiangxiensis sp. nov., a strictly anaerobic, propionate-producing bacterium isolated from rice paddy field. Archives of Microbiology, 196(3): 149155. https://doi.org/10.1007/S00203-013-0951-1/FIGURES/3 Reddy, T. B. K., Thomas, A. D., Stamatis, D., Bertsch, J., Isbandi, M., Jansson, J., Mallajosyula, J., Pagani, I., Lobos, E. A. and Kyrpides, N. C. 2015. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Research, 43(D1): D1099-D1106. https://doi.org/10.1093/NAR/GKU950 Schimel, J., Balser, T. C. and Wallenstein, M. 2007. Microbial stress-response physiology and its implications for ecosystem function. Ecology, 88(6): 13861394. https://doi.org/10.1890/06-0219 241

J. Environ. & Sociobiol. : 19(2) : 221-243, 2022, Ghosh et al. Scholten, E., Lukow, T., Auling, G., Kroppenstedt, R. M., Rainey, F. A. and Diekmann, H. 1999. Thauera mechernichensis sp. nov., an aerobic denitrifier from a leachate treatment plant. International Journal of Systematic Bacteriology, 49 Pt 3(3): 1045-1051. https://doi.org/10.1099/00207713-49-3-1045 Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A. and Harada, H. 2000. Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. International Journal of Systematic and Evolutionary Microbiology, 50 Pt 2(2): 771-779. https://doi.org/10.1099/00207713-50-2-771 Sharma, S., Szele, Z., Schilling, R., Munch, J. C. and Schloter, M. 2006. Influence of freeze-thaw stress on the structure and function of microbial communities and denitrifying populations in soil. Applied and Environmental Microbiology, 72(3): 2148-2154. https://doi.org/10.1128/AEM.72.3.2148-2154.2006 Slobodkina, G. B., Kovaleva, O. L., Miroshnichenko, M. L., Slobodkin, A. I., Kolganova, T. v., Novikov, A. A., van Heerden, E. and Bonch-Osmolovskaya, E. A. 2015. Thermoguttaterrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes. International Journal of Systematic and Evolutionary Microbiology, 65(Pt 3): 760-765. https://doi.org/10.1099/IJS.0.000009 Sohn, J. H., Kwon, K. K., Kang, J. H., Jung, H. B. and Kim, S. J. 2004. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. International Journal of Systematic and Evolutionary Microbiology, 54(5): 14831487. https://doi.org/10.1099/IJS.0.02945-0/CITE/REFWORKS Suzina, N. E., Mulyukin, A. L., Kozlova, A. N., Shorokhova, A. P., Dmitriev, V. v., Barinova, E. S., Mokhova, O. N., El’-Registan, G. I. and Duda, V. I. 2004. Ultrastructure of Resting Cells of Some Non-Spore-Forming Bacteria. Microbiology, 73(4): 435-447. https://doi.org/10.1023/B:MICI.0000036990.94039. af Tamang, M. D., Sunwoo, H. and Jeon, B. 2017. Phage-mediated dissemination of virulence factors in pathogenic bacteria facilitated by antibiotic growth promoters in animals: A perspective. Animal Health Research Reviews, 18(2): 160-166. https://doi.org/10.1017/S1466252317000147 Tenover, F. C. 2006. Mechanisms of Antimicrobial Resistance in Bacteria. The American Journal of Medicine, 119(6): S3-S10. https://doi.org/10.1016/j. amjmed.2006.03.011 Turki, Y., Mehri, I., Lajnef, R., Rejab, A.B., Khessairi, A., Cherif, H., Ouzari, H.I., and Hassen, A. 2017. Biofilms in bioremediation and wastewater treatment: characterization of bacterial community structure and diversity during seasons in municipal wastewater treatment process. Environmental Science and Pollution Research, 24: 3519-3530. 242

Microbial enrichment in global wastewater niches under impact of climate.... Vitousek, P. M., Menge, D. N. L., Reed, S. C. and Cleveland, C. C. 2013. Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1621). https://doi.org/10.1098/RSTB.2013.0119 Wattam, A. R., Davis, J. J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., Conrad, N., Dietrich, E. M., Disz, T., Gabbard, J. L., Gerdes, S., Henry, C. S., Kenyon, R. W., Machi, D., Mao, C., Nordberg, E. K., Olsen, G. J., Murphy-Olson, D. E., Olson, R., Stevens, R. L. 2017. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Research, 45(D1), D535-D542. https://doi.org/10.1093/nar/gkw1017 Willems, A. and Gillis, M. 2015. Acidovorax. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-16. https://doi.org/10.1002/9781118960608.GBM00943 Yang, G. Q., Zhang, J., Kwon, S. W., Zhou, S. G., Han, L. C., Chen, M., Ma, C. and Li, Z. 2013. Thauerahumireducens sp. nov., a humus-reducing bacterium isolated from a microbial fuel cell. International Journal of Systematic and Evolutionary Microbiology, 63(Pt 3): 873-878. https://doi.org/10.1099/IJS.0.040956-0 Zhang, L., Qiu, X., Huang, L., Xu, J., Wang, W., Li, Z., Xu, P. and Tang, H. 2021. Microbial degradation of multiple PAHs by a microbial consortium and its application on contaminated wastewater. Journal of Hazardous Materials, 419: 126524. https://doi.org/10.1016/J.JHAZMAT.2021.126524 Zhao, Z., Lin, Q., Zhou, Y., Feng, Y., Huang, Q. and Wang, X. 2021. Pollutant removal from municipal sewage by a microaerobic up-flow oxidation ditch coupled with micro-electrolysis. Royal Society Open Science, 8.

243