Research Progress of Acidobacteria Ecology in Soils

doi:10.13560/j.cnki.biotech.bull.1985.2016.02.002

Abstract

Abstract: The phylum Acidobacteria is one of the most important bacterial groups in soils.Based on analysis of 16S rRNA gene sequences, the number of Acidobacteria generally represents about 20% of total soil bacterial communities, some of them even account for more than 50%, which suggests that Acidobacteria play important roles in soil ecological process.In this paper, we reviewed the research progress of Acidobacteria ecology in soils from several aspects, such as effects of plant types, altitude, nitrogen fertilizer and CO₂ enrichment on the distribution of Acidobacteria, as well as rhizosphere effects of Acidobacteria, etc.The relationships between distributions of different taxonomic level Acidobacteria and environmental factors were summarized.The potential ecological functions of Acidobacteria were also presented in this paper.In the end of this paper, the importance for future study of Acidobacteria, such as reinforcement of isolation and pure culture, refinement of molecular ecological research, and adoption of metagenomics and single-cell sequencing approaches were also addressed.

Key words: Acidobacteria, microbial ecology, subdivision, 16S rRNA gene, high-throughput sequencing

WANG Guang-hua, LIU Jun-jie, YU Zhen-hua, WANG Xin-zhen, JIN Jian, LIU Xiao-bing. Research Progress of Acidobacteria Ecology in Soils[J]. Biotechnology Bulletin, 2016, 32(2): 14-20.

References

[1] Kishimoto N, Kosako Y, Tano T.Acidobacterium capsulatum gen.nov., sp.nov.：an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment[J].Current Microbiology, 1991, 22：1-7.
[2] Ludwig W, Bauer SH, Bauer M, et al.Detection and in situ identification of representatives of a widely distributed new bacterial phylum[J].FEMS Microbiology Letters, 1997, 153：181-190.
[3] Barns SM, Takala SL, Kuske CR.Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment[J].Applied and Environmental Microbiology, 1999, 65：1731-1737.
[4] Janssen PH, Yates PS, Grinton BE, et al.Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia[J].Applied and Environmental Microbiology, 2002, 68：2391-2396.
[5] Jones RT, Robeson MS, Lauber CL, et al.A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses[J].The ISME Journal, 2009, 3：442-453.
[6] Lee SH, Ka JO, Cho JC.Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil[J].FEMS Microbiology Letter, 2008, 285：263-269.
[7] Hugenholtz P, Goebel BM, Pace NR.Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity[J].Journal of Bacteriology, 1998, 180：4765-4774.
[8] Xiong J, Liu Y, Lin X, et al.Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau[J].Environmental Microbiology, 2012, 14：2457-2466.
[9] Barns SM, Cain EC, Sommerville L, et al.Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum[J].Applied and Environmental Microbiology, 2007, 73：3113-3116.
[10] Naether A, Foesel BU, Naegele V, et al.Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils[J].Apply Environmental Microbiology, 2012, 78：7398-7406.
[11] Fierer N, Bradford MA, Jackson RB.Toward an ecological classific-ation of soil bacteria[J].Ecology, 2007, 88：1354-1364.
[12] M?nnist? MK, Tiirola M, H?ggblom MM, et al.Bacterial commun-ities in Arctic fjelds of Finnish Lapland are stable but highly pH de-pendent[J].FEMS Microbiology Ecology, 2007, 59：452-465.
[13] Lauber CL, Strickland MS, Bradford MA, et al.The influence of soil properties on the structure of bacterial and fungal communities across land-use types[J].Soil Biology and Biochemistry, 2008, 40：2407-2415.
[14] Chu HY, Fierer N, Lauber CL, et al.Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes[J].Environmental Microbiology, 2010, 12：2998-3006.
[15] Griffiths RI, Thomson BC, James P, et al.The bacterial biogeography of British soils[J].Environmental Microbiology, 2011, 13：1642-1654.
[16] Zhang Y, Cong J, Lu H, et al.Community structure and elevational diversity patterns of soil Acidobacteria[J].Journal of Environm-ental Sciences, 2014, 26：1717-1724.
[17] Liu JJ, Sui YY, Yu ZH, et al.Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China[J].Soil Biology and Biochemistry, 2015, 83：29-39.
[18] 王春香, 田宝玉, 吕睿瑞, 等.西双版纳地区热带雨林土壤酸杆菌(Acidobacteria)群体结构和多样性分析[J].微生物学通报, 2010, 37：24-29.
[19] Navarrete AA, Kuramae EE, de Hollander M, et al.Acidobacterial community responses to agricultural management of soybean in Amazon forest soils[J].FEMS Microbiol Ecology, 2013, 83：607-621.
[20] Fierer N, McCain CM, Meir P, et al. Microbes do not follow the elevational diversity patterns of plants and animals[J].Ecology, 2011, 92：797-804.
[21] Shen CC, Xiong JB, Zhang HY, et al.Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain[J].Soil Biology and Biochemistry, 2003, 57：204-211.
[22] Fierer N, Lauber CL, Ramirez KS, et al.Comparative metagenomic, phylogenetic and physiological analyses of soil microbial commu-nities across nitrogen gradients[J].The ISME Journal, 2012, 6：1007-1017.
[23] Campbell BJ, Polson SW, Hanson TE, et al. The effect of nutrient deposition on bacterial communities in Arctic tundra soil[J].Environmental Microbiology, 2010, 12：1842-1854.
[24] Ramirez KS, Craine JM, Fierer N.Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes[J].Global Change Biology, 2012, 18：1918-1927.
[25] Lesaulnier C, Papamichail D, McCorkle S, et al.Elevated atmospheric CO₂ affects soil microbialdiversity associated with trembling aspen[J].Enviromental Microbiology, 2008, 10：926-941.
[26] Austin EE, Castro HF, Sides KE, et al.Assessment of 10 years of CO₂ fumigation on soil microbial communities and function in a sweetgum plantation[J].Soil Biology and Biochemistry, 2009, 41：514-520.
[27] Dunbar J, Eichorst SA, Gallegos-Graves LV, et al.Common bacter-ial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide[J].Evironmental Microbiology, 2012, 14：1145-1158.
[28] Dunbar J, Gallegos-Graves LV, Steven B, et al.Surface soil fungal and bacterial communities in aspen stands are resilient to eleven years of elevated CO₂ and O₃[J].Soil Biology and Biochemistry, 2014, 76：227-234.
[29] Gschwendtner S, Leberecht M, Engel M, et al. Effects of elevated atmospheric CO₂ on microbial community structure at the plant-soil interface of young beech trees(Fagus sylvatica L.)grown at two sites with contrasting climatic conditions[J].Microbial Ecology, 2015, 69：867-878.
[30] Deng Y, He Z, Xu M, et al.Elevated carbon dioxide alters the stru-cture of soil microbial communities[J].Applied and Environme-ntal Microbiology, 2012, 78：2991-2995.
[31] Uroz S, Buée M, Murat C, et al.Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil[J].Environmental Microbiology Reports, 2010, 2：281-288.
[32] da Rocha UN, van Elsas JD, van Overbeek LS.Real-time PCR detection of Holophagae(Acidobacteria)and Verrucomicrobia subdivision 1 groups in bulk and leek(Allium porrum)rhizosphere soils[J].Journal of Microbiological Methods, 2010, 83：141-148.
[33] Kielak A, Pijl AS, van Veen JA, et al. Phylogenetic diversity of Acidobacteria in a former agricultural soil[J].The ISME Journal, 2009, 3：378-382.
[34] Pankratov TA, Kirsanova LA, Kaparullina EN, et al.Telmatobacter bradus gen.nov., sp.nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria and emended description of Acidobacterium capsulatum Kishimoto et al.1991[J].International Journal of Systematic and Evolutionary Microbiology, 2012, 62：430-437.
[35] Eichorst SA, Kuske CR, Schmidt TM.Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria[J].Applied Environmental Microbiology, 2011, 77：586-596.
[36] Pankratov TA, Ivanova AO, Dedysh SN, et al. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat[J].Environmental Microbiology, 2011, 13：1800-1814.
[37] Kanokratana P, Uengwetwanit T, Rattanachomsri U, et al.Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis[J].Microbial Ecology, 2011, 61：518-528.
[38] Lu SP, Gischkat S, Reiche M, et al.Ecophysiology of Fe-cycling bacteria in acidic sediments[J].Applied and Environmental Microbiology, 2010, 76：8174-8183.
[39] Coates JD, Ellis DJ, Gaw CV, et al.Geothrix fermentans gen.nov., sp nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer[J].International Journal of Systematic Bacteriology, 1999, 49：1615-1622.
[40] Bl?the M, Akob DM, Kostka JE, et al. pH gradient-induced hetero-geneity of Fe(III)-reducing microorganisms in coal mining-associated lake sediments[J].Applied and Environmental Microbiology, 2008, 74：1019-1029.
[41] Coupland K, Johnson DB.Evidence that the potential for dissimilatory ferric iron reduction is widespread among acidophilic heterotrophic bacteria[J].FEMS Microbiology Letters, 2008, 279：30-35.
[42] Bryant DA, Costas AMG, Maresca JA, et al.Candidatus Chloraci-dobacterium thermophilum：An aerobic phototrophic acidobacte-rium[J].Science, 2007, 317：523-526.
[43] Müh F, Madjet MEA, Adolphs J, et al.α-Helices direct excitation energy flow in the Fenna-Matthews-Olson protein[J].Procee-dings of the National Academy of Sciences of theUnited StatesofAmerica, 2007, 104：16862-16867.
[44] Pankratov TA, Serkebaeva YM, Kulichevskaya IS, et al.Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat[J].ISME Journal, 2008, 2：551-560.
[45] Radajewski S, Webster G, Reay DS, et al. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing[J].Microbiology, 2002, 148：2331-2342.
[46] Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L.Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington[J].ISME Journal, 2008, 2：696-706.