Microbial Diversity and Community Structure in Alpine Stream Soil

References

• Abilio GS, Cupelo ACG, Rezende CE. 2012. Heavy metal distribution in sediments of an offshore exploration area, Santos basin, Brazil. Geochimica Brasiliensis 20:1.
   Google Scholar
• Adnan M, Zahir S, Fahad S, Arif M, Mukhtar A, Imtiaz AK, Ishaq AM, Abdul B, Hidayat U, Muhammad A, et al. 2018. Phosphatesolubilizing bacteria nullify the antagonistic effect of soil calcification on bioavailability of phosphorus in alkaline soils. Sci Rep 8:4339.
   PubMed Web of Science ®Google Scholar
• Ali S, Gao J, Begum F, Rasool A, Ismail M, Cai Y, Ali S, Ali S. 2017. Health assessment using aqua-quality indicators of alpine streams (Khunjerab National Park), Gilgit, Pakistan. Environ Sci Pollut Res Int 24(5):4685–4698.
   PubMed Web of Science ®Google Scholar
• Anjana K, Kaushik A, Kiran B, Nisha R. 2007. Biosorption of Cr(VI) by immobilized biomass of two indigenous strains of cyanobacteria isolated from metal contaminated soil. J Hazard Mater 148(1–2):383–386.
   PubMed Web of Science ®Google Scholar
• Arriagada C, Aranda E, Sampedro I, Garcia-Romera I, Ocampo JA. 2009. Interactions of Trametes versicolor, Coriolopsis rigida and the arbuscular mycorrhizal fungus Glomus deserticola on the copper tolerance of Eucalyptus globulus. Chemosphere 77(2):273–281.
   PubMed Web of Science ®Google Scholar
• Ashley P, Craw D, Graham B, Chappell D. 2003. Environmental mobility of metals around mesothermal stibnite deposits, New South Wales, Australia and southern New Zealand. J Geochem Expl 77(1):1–14.
   Web of Science ®Google Scholar
• Babu GA, Shea PJ, Oh B. 2014. Trichoderma sp. PDR1-7 promotes Pinus sylvestris reforestation of lead-contaminatedmine tailing sites. Sci Total Environ 477:561–567.
   Google Scholar
• Baker BJ, Banfield JF. 2003. Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44:139–152.
   Google Scholar
• Bao Z, Sato Y, Fujimura R, Ohta H. 2014. Alsobacter metallidurans gen. nov., sp nov., a thallium-tolerant soil bacterium in the order Rhizobiales. Int J Syst Evol Microbiol 64(Pt 3):775–780.
   PubMedGoogle Scholar
• Bishop DL, Prindle SE, Johnson JH. 2008. Salmon river wild young of year Chinook salmon seining program. Albany, NY: New York State Department of Environmental Conservation .
   Google Scholar
• Cao DJ, Shi XD, Li H, Xie PP, Zhang HM, Deng JW, Liang YG. 2015. Effects of lead on tolerance, bioaccumulation, and antioxidative defense system of green algae, Cladophora. Ecotoxicol Environ Saf 112:231–237.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Craw D, Falconer D, Youngson J. 2003. Environmental arsenopyrite stability and dissolution: theory, experiment, and field observations. Chem Geol 199(1-2):1.:71–82.
   Web of Science ®Google Scholar
• Crump BC, Amaral-Zettler LA, Kling GW. 2012. Microbial diversity in arctic freshwaters is structured by innoculation of microbes from soils. Isme J 6(9):1629–1639.
   PubMed Web of Science ®Google Scholar
• Dos Santos DA, Molineri C, Reynaga MC, Basualdo C. 2011. Which index is the best to assess stream health?. Ecol Ind 11(2):582–589.
   Web of Science ®Google Scholar
• Edgar RC. 2018. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. Peer J. 4645–4652.
   Web of Science ®Google Scholar
• Fahad S, Bano A. 2012. Effect of salicylic acid on physiological and biochemical characterization of maize grown in saline area. Pak J Bot 44:1433–1438.
   Web of Science ®Google Scholar
• Fahad S, Chen Y, Saud S, Wang K, Xiong D, Chen C, Wu C, Shah F, Nie L, Huang J. 2013. Ultraviolet radiation effect on photosynthetic pigments, biochemical attributes, antioxidant enzyme activity and hormonal contents of wheat. J Food Agric Environ 11(3&4):1635–1641.
   Google Scholar
• Fahad S, Hussain S, Bano A, Saud S, Hassan S, Shan D, Khan FA, Khan F, Chen Y, Wu C, et al. 2015. Potential role of phytohormones and plant growth-promoting rhizobacteria in abiotic stresses: consequences for changing environment. Environ Sci Pollut Res Int 22(7):4907–4921.
   PubMed Web of Science ®Google Scholar
• Fahad S, Hussain S, Saud S, Hassan S, Ihsan Z, Shah AN, Wu C, Yousaf M, Nasim W, Alharby H. 2016. Exogenously applied plant growth regulators enhance the morphophysiological growth and yield of rice under high temperature. Front Plant Sci 7:1250.
   PubMed Web of Science ®Google Scholar
• Fahad S, Hussain S, Saud S, Hassan S, Tanveer M, Ihsan MZ, Shah AN, Ullah A, Nasrullah KF, Ullah S, et al. 2016. A combined application of biochar and phosphorus alleviates heat-induced adversities on physiological, agronomical and quality attributes of rice. Plant Physiol Biochem 103:191–198.
   PubMed Web of Science ®Google Scholar
• Fahad S, Muhammad ZI, Abdul K, Ihsanullah D, Saud S, Saleh A, Wajid N, Muhammad A, Imtiaz AK, Chao W, et al. 2018. Consequences of high temperature under changing climate optima for rice pollen characteristics–concepts and perspectives. Archives Agron Soil Sci 64(11):1473–1488.
   Web of Science ®Google Scholar
• Fahad S, Nie L, Chen Y, Wu C, Xiong D, Saud S, Hongyan L, Cui K, Huang J. 2015. Crop plant hormones and environmental stress. Sustain Agric Rev 15:371–400.
   Google Scholar
• Faisal AAH, Al-Wakel SFA, Assi HA, Naji LA, Naushad M. 2020. Waterworks sludge-filter sand permeable reactive barrier for removal of toxic lead ions from contaminated groundwater. J Water Process Eng 33:101112.
   Web of Science ®Google Scholar
• Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103(3):626–631.
   PubMed Web of Science ®Google Scholar
• Filella M, Belzile N, Chen YW. 2002. Antimony in the environment: a review focused on natural waters I. Occur. Earth Sci Rev 57(1-2):125–176.
   Web of Science ®Google Scholar
• Hu Q, Qi H, Zeng J, Zhang H. 2007. Bacterial diversity in soils around a lead and zinc mine. J Environ Sci China 19(1):74–79.
   PubMedGoogle Scholar
• Huang Y, Li H, Rensing C, Zhao K, Johnstone L, Wang G. 2012. Genome sequence of the facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium Acidovorax sp. strain NO1. J Bacteriol 194(6):1635–1646.
   PubMed Web of Science ®Google Scholar
• Johnson DB, Hallberg KB. 2005. Acid mine drainage remediation options: a review. Sci Total Environ 338(1–2):3–14.
   PubMed Web of Science ®Google Scholar
• Kalin M, Wheeler WN, Meinrath G. 2005. The removal of uranium from mining waste water using algal/microbial biomass. J Environ Radioact 78(2):151–177.
   PubMed Web of Science ®Google Scholar
• Khan A, Tan DKY, Munsif F, Afridi MZ, Shah F, Wei F, Fahad S, Zhou R. 2017. Nitrogen nutrition in cotton and control strategies for greenhouse gas emissions: a review. Environ Sci Pollut Res Int 24(30):23471–23487.
   PubMed Web of Science ®Google Scholar
• Lefebvre DD, Kelly D, Budd K. 2007. Biotransformation of Hg(II) by cyanobacteria. Appl Environ Microbiol 73 (1):243–249.
   PubMed Web of Science ®Google Scholar
• Li J, Sun W, Wang S, Sun Z, Lin S, Peng X. 2014. Bacteria diversity, distribution and insight into their role in S and Fe biogeochemical cycling during black shale weathering. Environ Microbiol 16(11):3533–3547.
   PubMed Web of Science ®Google Scholar
• Ling Z, Liu X, Jia X, Cheng Y, Luo Y, Yuan L, Wang Y, Zhao C, Guo S, Li L, et al. 2014. Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children. Sci Rep 4:7485–7495.
   PubMed Web of Science ®Google Scholar
• Majzlan J, Lalinska B, Chovan M, Blass U, Brecht B, Gottlicher J, Steininger R, Hug K, Ziegler S, Gescher J. 2011. A mineralogical, geochemical, and microbiological assessment of the antimony-and arsenic-rich neutral mine drainage tailings near Pezinok, Slovakia. Am Mineral 96(1):1–13.
   Web of Science ®Google Scholar
• Margesin R, Płaza GA, Kasenbacher S. 2011. Characterization of bacterial communities at heavy-metal-contaminated sites. Chemosphere 82(11):1583–1588.
   PubMed Web of Science ®Google Scholar
• McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee- Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL. 2013. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci USA 110:2390–2399.
   PubMed Web of Science ®Google Scholar
• Muhammad Z, Abdul MK, Abdul MS, Kenneth BM, Muhammad S, Shahen S, Ibadullah J, Fahad S. 2019. Performance of Aeluropus lagopoides (mangrove grass) ecotypes, a potential turfgrass, under high saline conditions. Environ Sci Pollut Res Int 26(13):13410–13421.
   PubMed Web of Science ®Google Scholar
• Murciego AM, Sanchez AG, Gonzalez MR, Gil EP, Gordillo CT, Fernandez JC, Triguero TB. 2007. Antimony distribution and mobility in topsoils and plants (Cytisus striatus, Cistus ladanifer and Dittrichia viscosa) from polluted Sb-mining areas in Extremadura (Spain). Environ Pollut 145(1):15–21.
   PubMed Web of Science ®Google Scholar
• Muthusaravanan S, Sivarajasekar N,·Vivek JS, Paramasivan T, Naushad M, Prakashmaran J, Gayathri V, Al- Duaij OK. 2018. Phytoremediation of heavy metals: mechanisms, methods and enhancements. Environ Chem Lett 16 (4):1339–1359.
   Web of Science ®Google Scholar
• Nakamaru Y, Tagami K, Uchida S. 2006. Antimony mobility in Japanese agricultural soils and the factors affecting antimony sorption behavior. Environ Pollut. 141(2):321–326.
   PubMed Web of Science ®Google Scholar
• Oves M, Khan MS, Zaidi A. 2013. Biosorption of heavy metals by Bacillus thuringiensis strain OSM29 originating from industrial effluent contaminated north Indian soil. Saudi J Biol Sci. 20(2):121–129.
   PubMed Web of Science ®Google Scholar
• Park S, Jung YT, Won SM, Lee JS, Yoon JH. 2015. Demequina activiva sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 65(7):2042–2047.
   PubMedGoogle Scholar
• Pokrovsky O, Martinez R, Kompantzeva E, Shirokova L. 2014. Surface complexation of the phototrophic anoxygenic non-sulfur bacterium Rhodopseudomonas palustris. Chem Geol 383:51–62.
   Web of Science ®Google Scholar
• Rasool A, Xiao TF. 2018. The response of microbial communities to elevated thallium contamination in river sediments. Geomicrobiol J 35(10):1–15.
   Web of Science ®Google Scholar
• Ren G, Zhang H, Lin X, Zhu J, Jia Z. 2014. Response of phyllosphere bacterial communities to elevated CO2 during rice growing season. Appl Microbiol Biotechnol 98(22):9459–9471.
   PubMed Web of Science ®Google Scholar
• Saud S, Fahad S, Cui G, Chen Y, Anwar S. 2020. Determining nitrogen isotopes discrimination under drought stress on enzymatic activities, nitrogen isotope abundance and water contents of Kentucky bluegrass. Sci Rep 10(1):6415.
   PubMed Web of Science ®Google Scholar
• Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AKT, et al. 2015. Bacterial diversity along a 2600 km river continuum. Environ Microbiol 17(12):4994–5007.
   PubMed Web of Science ®Google Scholar
• Savonina EY, Fedotov P, Wennrich R. 2012. Fractionation of Sb and As in soil and sludge samples using different continuous-flow extraction techniques. Anal Bioanal Chem 403(5):1441–1449.
   PubMed Web of Science ®Google Scholar
• Schippers A, Breuker A, Blazejak A, Bosecker K, Kock D, Wright T. 2010. The biogeochemistry and microbiology of sulfidic mine waste and bioleaching dumps and heaps, and novel Fe.II.-oxidizing bacteria. Hydrometallurgy 104(3-4):342–350.
   Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541.
   PubMed Web of Science ®Google Scholar
• Sharma G, Naushad M. 2020. Adsorptive removal of noxious cadmium ions from aqueous medium using activated carbon/zirconium oxide composite: isotherm and kinetic modelling. J Mol Liq 310:113025.
   Web of Science ®Google Scholar
• Sorokin DY, Tourova T, Mußmann M, Muyzer G. 2008. Dethiobacter alkaliphilus gen. nov.sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes. Extremophiles 12(3):431–439.
   PubMed Web of Science ®Google Scholar
• Sousa NR, Ramos MA, Marques APGC, Castro PML. 2012. The effect of ectomycorrhizal fungi forming symbiosis with Pinus pinaster seedlings exposed to cadmium. Sci Total Environ 414:63–67.
   PubMed Web of Science ®Google Scholar
• Staley C, Unno T, Gould T, Jarvis B, Phillips J, Cotner J, Sadowsky M. 2013. Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol 115(5):1147–1158.
   PubMed Web of Science ®Google Scholar
• Sun W, Sun X, Cupples AM. 2014. Presence, diversity and enumeration of functional genes (bssA and bamA) relating to toluene degradation across a range of redox conditions and inoculum sources. Biodegradation 25(2):189–203.
   PubMed Web of Science ®Google Scholar
• Sun W, Xiao E, Dong Y, Tang S, Krumins V, Ning Z, Sun M, Zhao Y, Wu S, Xiao T. 2016. Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China. Sci Total Environ 550:297–308.
   PubMed Web of Science ®Google Scholar
• Sun M, Xiao T, Ning Z, Xiao E, Sun W. 2015. Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water. Appl Microbiol Biotechnol 99(6):2911–2922.
   PubMed Web of Science ®Google Scholar
• Sun JL, Zou X, Ning ZP, Sun M, Peng JQ, Xiao TF. 2012. Culturable microbial groups and thallium-tolerant fungi in soils with high thallium contamination. Sci Total Environ 441:258–264.
   PubMed Web of Science ®Google Scholar
• Wang Y, Shi J, Wang H, Lin Q, Chen X, Chen Y. 2007. The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter. Ecotoxicol Environ Saf 67(1):75–81.
   PubMed Web of Science ®Google Scholar
• Wilson N, Craw D, Hunter K. 2004. Antimony distribution and environmental mobility at an historic antimony smelter site, New Zealand. Environ Pollut 129 (2):257–266.
   PubMed Web of Science ®Google Scholar
• Wu F, Geng Y, Tian X, Zhong S, Wu W, Yu S, Xiao S. 2018. Responding climate change: A bibliometric review on urban environmental governance, J Cleaner Prod 204: 344–354.
   Google Scholar
• Wu G, Shang J, Pan L, Wang Z. 2012. Heavy metals in surface sediments from nine estuaries along the coast of Bohai Bay, Northern China. Mar Pollut Bull 82:1:194–200.
   Web of Science ®Google Scholar
• Xi J, He M, Lin C. 2010. Adsorption of antimony(V) on kaolinite as a function of pH, ionic strength and humic acid. Environ Earth Sci 60 (4):715–722.
   Web of Science ®Google Scholar
• Xiao EZ, Krumins V, Dong YR, Xiao TF, Ning ZP, Xiao QX, Sun WM. 2016. Microbial diversity and community structure in an antimony-rich tailings dump. Appl Microbiol Biotechnol 100(17):7751–7763.
   PubMed Web of Science ®Google Scholar
• Xiao E, Krumins V, Xiao T, Dong Y, Tang S, Ning Z, Huang Z, Sun W. 2017. Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic. Environ Pollut 221:244–255.
   PubMed Web of Science ®Google Scholar
• Xiao TF, Yang F, Li SH, Zheng BS, Ning ZP. 2012. Thallium pollution in China: a geoenvironmental perspective. Sci Total Environ 421-422:51–58.
   PubMed Web of Science ®Google Scholar
• Zahida Z, Hafiz FB, Zulfiqar AS, Ghulam MS, Fahad S, Muhammad RA, Hafiz MH, Wajid N, Muhammad S. 2017. Effect of water management and silicon on germination, growth, phosphorus and arsenic uptake in rice. Ecotoxicol Environ Saf 144:11–18.
   PubMed Web of Science ®Google Scholar
• Zhang N, Wan S, Li L, Bi J, Zhao M, Ma K. 2008. Impacts of urea N addition on soil microbial community in a semi-arid temperate steppe in northern China. Plant Soil 311(1-2):19–28.
   Web of Science ®Google Scholar
• Zhang F-P, Li C-F, Tong L-G, Yue L-X, Li P, Ciren Y-J, Cao C-G. 2010. Response of microbial characteristics to heavy metal pollution of mining soils in central Tibet. China. Appl Soil Ecol 45(3):144–151.
   Web of Science ®Google Scholar