Vertical and island-scale structuring of bacterial and archaeal communities in Pinus merkusii forest soils
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Abstract. Nugroho RA, van Straalen NM, Röling WFM. 2026. Vertical and island-scale structuring of bacterial and archaeal communities in Pinus merkusii forest soils. Biodiversitas 27 (3): d270313. https://doi.org/10.13057/biodiv/d270313. Environmental and spatial processes contribute to the structuring of soil microbial communities, but the relative importance of vertical and horizontal gradients is poorly understood in tropical archipelagic forests. The vertical and spatial distributions of bacterial and archaeal communities were examined in Pinus merkusii forest soils across 12 sites on five Indonesian islands (36 composite samples). Litter (L), fragmented litter (F), and mineral (M) soil layers were analyzed using denaturing gradient gel electrophoresis (DGGE) to characterize dominant community profiles. Community dissimilarity was assessed using Mantel and partial Mantel tests, and compositional variance was assessed using PERMANOVA. Bacterial communities were strongly vertically stratified. Mantel tests showed significant correlations between community dissimilarity and soil layer (r = 0.52, p < 0.001) and geographic distance (r = 0.60, p < 0.001), which remained significant in partial correlations. PERMANOVA indicated that soil layer explained 43.5% of the variation (pseudo-R2 = 0.435, p < 0.001), whereas island identity explained 15.1% (pseudo-R2 = 0.151, p = 0.0135). In contrast, archaeal communities showed no significant association with either geographic distance (r = −0.03, p = 0.68) or soil layer (r = −0.04, p = 0.80). In contrast, PERMANOVA revealed strong differentiation among island identity (pseudo-R2 = 0.375, p = 0.0045). These findings reveal contrasting domain-specific spatial organization of microbial communities, with bacteria primarily structured by vertical habitat differentiation and distance–decay patterns, whereas archaea communities are mainly differentiated at the island scale. The results highlight distinct spatial scales of organization for major microbial domains in tropical forest soils. However, the absence of environmental physicochemical measurements limits direct identification of the environmental drivers underlying these patterns.
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Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P. 2018. Structure and function of the global topsoil microbiome. Nature 560 (7717): 233-237. https://doi.org/10.1038/s41586-018-0386-6.
Barbour KM, Barrón‐Sandoval A, Walters KE, Martiny JBH. 2023. Towards quantifying microbial dispersal in the environment. Environ Microbiol 25 (1): 137-142. https://doi.org/10.1111/1462-2920.16270.
Carvajal DE, Loayza AP, Squeo FA. 2023. Functional diversity and spatial association analyses at different spatial scales reveal no changes in community assembly processes along an aridity gradient in the Atacama Desert. Sci Rep 13 (1): 19905. https://doi.org/10.1038/s41598-023-47187-5.
Chen S, Zhang Y, Ma J, Bai M, Chen Y, Guo J, Chen L. 2025. Environmental effects on bacterial community assembly in arid and semi-arid grasslands. Microorganisms 13 (8): 1934. https://doi.org/10.3390/microorganisms13081934.
Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N. 2018. A global atlas of the dominant bacteria found in soil. Science 359 (6373): 320-325. https://doi.org/10.1126/science.aap9516.
Ezzat L, Peter H, Bourquin M, Busi SB, Michoud G, Fodelianakis S, Kohler TJ, Lamy T, Geers A, Pramateftaki P, Baier F, Marasco R, Daffonchio D, Deluigi N, Wilmes P, Styllas M, Schön M, Tolosano M, De Staercke V, Battin TJ. 2025. Diversity and biogeography of the bacterial microbiome in glacier-fed streams. Nature 637 (8046): 622-630. https://doi.org/10.1038/s41586-024-08313-z.
Fanin N, Barantal S, Fromin N, Schimann H, Schevin P, Hättenschwiler S. 2012. Distinct microbial limitations in litter and underlying soil revealed by carbon and nutrient fertilization in a tropical rainforest. PLoS One 7 (12): e49990. https://doi.org/10.1371/journal.pone.0049990.
Feng M, Tripathi BM, Shi Y, Adams JM, Zhu Y, Chu H. 2019. Interpreting distance‐decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales. Microbiology 8 (9): e00851. https://doi.org/10.1002/mbo3.851.
Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Singan V, Vogel J, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW. 2020. Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nat Commun 11 (1): 34. https://doi.org/10.1038/s41467-019-13913-9.
He L, Sun X, Li S, Zhou W, Chen Z, Bai X. 2023. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. Sci Total Environ 869: 161754. https://doi.org/10.1016/j.scitotenv.2023.161754.
Hu L, Wang X, Song X, Dai D, Ding L, Degen AA, Wang C. 2023. Vertical patterns of soil bacterial and fungal communities along a soil depth gradient in a natural Picea crassifolia forest in Qinghai Province, China. Forests 14 (5): 1016. https://doi.org/10.3390/f14051016.
Jiao S, Chen W, Wang J, Du N, Li Q, Wei G. 2018. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome 6 (1): 146. https://doi.org/10.1186/s40168-018-0526-0.
Liu H, Han H, Zhang C, Yu X, Nie W, Shao Q, Yang P, Li X, Yang Y, Cao H. 2023. Patterns of bacterial distance decay and community assembly in different land-use types as influenced by tillage management and soil layers. Ecotoxicol Environ Saf 266: 115595. https://doi.org/10.1016/j.ecoenv.2023.115595.
Liu W, Guo S, Zhang H, Chen Y, Shao Y, Yuan Z. 2024. Effect of altitude gradients on the spatial distribution mechanism of soil bacteria in temperate deciduous broad-leaved forests. Microorganisms 12 (6): 1034. https://doi.org/10.3390/microorganisms12061034.
Laumonier Y. 1997. The Vegetation and Physiography of Sumatra. Kluwer Academic, Dordrecht. https://doi.org/10.1007/978-94-009-0031-8.
Logares R, Tesson SVM, Canbäck B, Pontarp M, Hedlund K, Rengefors K. 2018. Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environ Microbiol 20 (6): 2231-2240. https://doi.org/10.1111/1462-2920.14265.
Lv J, Niu Y, Yuan R, Wang S. 2021. Different responses of bacterial and archaeal communities in river sediments to water diversion and seasonal changes. Microorganisms 9 (4): 782. https://doi.org/10.3390/microorganisms9040782.
Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. 2021. Soil depth matters: Shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 97 (3): fiab022. https://doi.org/10.1093/femsec/fiab022.
Muneer MA, Hou W, Li J, Huang X, ur Rehman Kayani M, Cai Y, Yang W, Wu L, Ji B, Zheng C. 2022. Soil pH: A key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard. BMC Microbiol 22 (1): 38. https://doi.org/10.1186/s12866-022-02452-x.
Muyzer G, de Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59 (3): 695-700. https://doi.org/10.1128/aem.59.3.695-700.1993.
Muyzer G, Smalla K. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73 (1): 127-141. https://doi.org/10.1023/a:1000669317571.
Ning D, Deng Y, Tiedje JM, Zhou J. 2019. A general framework for quantitatively assessing ecological stochasticity. Proc Natl Acad Sci 116 (34): 16892-16898. https://doi.org/10.1073/pnas.1904623116.
Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Solymos P, Stevens MHH, Szoecs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Borman T, Carvalho G, et al. 2025. Package ‘vegan’. Community ecology package, version 2 (9): 1-295. https://cran.r-project.org/web/packages/vegan/index.html.
Ovreås L, Forney L, Daae FL, Torsvik V. 1997. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63 (9): 3367-3373. https://doi.org/10.1128/aem.63.9.3367-3373.1997.
Qiao H, Zeng Q, Martin F, Wang Q. 2025. Impact of the soil layer on the soil microbial diversity and composition of Pinus yunnanensis at the Ailao Mountains subtropical forest. Front Microbiol 16: 1558906. https://doi.org/10.3389/fmicb.2025.1558906.
Riddley M, Hepp S, Hardeep FNU, Nayak A, Liu M, Xing X, Zhang H, Liao J. 2025. Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems. Nat Commun 16 (1): 2337. https://doi.org/10.1038/s41467-025-57526-x.
Sun J, Zhou H, Cheng H, Chen Z, Wang Y. 2025. Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments. mLife 4 (2): 205-218. https://doi.org/10.1002/mlf2.70006.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Xu ZZ, Jiang L, Haroon MF, Kanbar J, Zhu Q, Song SJ, Kosciolek T, Bokulich NA, Lefler J, et al. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551 (7681): 457-463. https://doi.org/10.1038/nature24621.
Tian Q, Jiang Q, Huang L, Li D, Lin Q, Tang Z, Liu F. 2023. Vertical distribution of soil bacterial communities in different forest types along an elevation gradient. Microb Ecol 85 (2): 628-641. https://doi.org/10.1007/s00248-021-01949-8.
Tripathi BM, Stegen JC, Kim M, Dong K, Adams JM, Lee YK. 2018. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J 12 (4): 1072-1083. https://doi.org/10.1038/s41396-018-0082-4.
Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach A-L. 1999. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 65 (10): 4375-4384. https://doi.org/10.1128/aem.65.10.4375-4384.1999.
Wainwright BJ, Leon J, Vilela E, Hickman KJE, Caldwell J, Aimone B, Bischoff P, Ohran M, Morelli MW, Arlyza IS, Marwayana ON, Zahn G. 2024. Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria. Environ Microbiome 19 (1): 23. https://doi.org/10.1186/s40793-024-00568-3.
Walters KE, Barbour KM, Powers JM, Martiny JBH. 2025. Microbial dispersal into surface soil is limited on a meter scale. ISME J 19 (1): wraf169. https://doi.org/10.1093/ismejo/wraf169.
Whitten T, Soeriaatmadja RE, Afiff SA. 1996. Ecology of Java and Bali. Periplus Editions (HK) Limited, Singapore.
Wu P, Hu D, Guo J, L, J, Zhong Q, Cheng D. 2024. Unraveling the spatial-temporal distribution patterns of soil abundant and rare bacterial communities in China’s subtropical mountain forest. Front Microbiol 15: 1323887. https://doi.org/10.3389/fmicb.2024.1323887.
Yin Y, Xu W, Xu M, Wang Y, Liu H, Cao H, Wang F. 2026. Prokaryotic microbial diversity and community assembly in reclaimed coastal agricultural soils. Microorganisms 14 (1): 120. https://doi.org/10.3390/microorganisms14010120.
Zhang L, Yang J, Ge A-H, Xie W, Yao R, Wang X. 2024. Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China. J Environ Manag 370: 122977. https://doi.org/10.1016/j.jenvman.2024.122977.
Zheng B, Xiao Z, Liu J, Zhu Y, Shuai K, Chen X, Liu Y, Hu R, Peng G, Li J, Hu Y, Su Z, Fang M, Li J. 2024. Vertical differences in carbon metabolic diversity and dominant flora of soil bacterial communities in farmlands. Sci Rep 14 (1): 9445. https://doi.org/10.1038/s41598-024-60142-2.