Articles | Volume 8, issue 1
https://doi.org/10.5194/soil-8-149-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-8-149-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Network complexity of rubber plantations is lower than tropical forests for soil bacteria but not for fungi
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Chuan Yang
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Zhixiang Wu
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Bangqian Chen
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Xicai Zhang
Rubber Research Institute, Chinese Academy of Tropical Agricultural
Sciences, Danzhou 571737, Hainan, PR China
Hainan Danzhou Tropical Agro-ecosystem National Observation and Research
Station, Danzhou 571737, Hainan, PR China
Related authors
Guoyu Lan, Bangqian Chen, Chuan Yang, Rui Sun, Zhixiang Wu, and Xicai Zhang
Biogeosciences, 19, 1995–2005, https://doi.org/10.5194/bg-19-1995-2022, https://doi.org/10.5194/bg-19-1995-2022, 2022
Short summary
Short summary
Little is known about the impact of rubber plantations on diversity of the Great Mekong Subregion. In this study, we uncovered latitudinal gradients of plant diversity of rubber plantations. Exotic species with high dominance result in loss of plant diversity of rubber plantations. Not all exotic species would reduce plant diversity of rubber plantations. Much more effort should be made to balance agricultural production with conservation goals in this region.
Rui Sun, Guoyu Lan, Chuan Yang, Zhixiang Wu, Banqian Chen, and Klaus Fraedrich
Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-303, https://doi.org/10.5194/bg-2021-303, 2021
Manuscript not accepted for further review
Short summary
Short summary
A soil quality index (SQI) based on 21 soil properties was employed to assess soil quality changes from tropical rainforest (TR) to rubber plantations (RP) . The results showed that the SQI of RP decreased by 26.48 % compared to TR, while four investigated soil properties increased. The SQI of both the TR and RP showed significant spatial differences, which, under TR, was more sensitive to seasonal changes than those under RP.
Guoyu Lan, Bangqian Chen, Chuan Yang, Rui Sun, Zhixiang Wu, and Xicai Zhang
Biogeosciences, 19, 1995–2005, https://doi.org/10.5194/bg-19-1995-2022, https://doi.org/10.5194/bg-19-1995-2022, 2022
Short summary
Short summary
Little is known about the impact of rubber plantations on diversity of the Great Mekong Subregion. In this study, we uncovered latitudinal gradients of plant diversity of rubber plantations. Exotic species with high dominance result in loss of plant diversity of rubber plantations. Not all exotic species would reduce plant diversity of rubber plantations. Much more effort should be made to balance agricultural production with conservation goals in this region.
Rui Sun, Guoyu Lan, Chuan Yang, Zhixiang Wu, Banqian Chen, and Klaus Fraedrich
Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-303, https://doi.org/10.5194/bg-2021-303, 2021
Manuscript not accepted for further review
Short summary
Short summary
A soil quality index (SQI) based on 21 soil properties was employed to assess soil quality changes from tropical rainforest (TR) to rubber plantations (RP) . The results showed that the SQI of RP decreased by 26.48 % compared to TR, while four investigated soil properties increased. The SQI of both the TR and RP showed significant spatial differences, which, under TR, was more sensitive to seasonal changes than those under RP.
Cited articles
Adams, R. I., Miletto, M., Taylor, J. W., and Bruns, T. D.: Dispersal in
microbes: fungi in indoor air are dominated by outdoor air and show
dispersal limitation at short distances, ISME J., 7, 1262–1273, 2013.
Amato, K. R., Yeoman, C. J., Kent, A., Carbonero, F., Righini, N., Estrada,
A. E., Gaskins, H. R., Stumpf, R. M., Yildirim, S., Torralba, M., Gillis, M.,
Wilson, B. A., Nelson, K. E., White, B. A., and Leigh, S. R.: Habitat
degradation impacts primate gastrointestinal microbiomes, ISME J., 7,
1344–1353, 2013.
Bach, E. M., Williams, R. J., Hargreaves, S. K., Yang, F., and Hofmockel, K.
S.: Greatest soil microbial diversity found in micro-habitats, Soil Biol.
Biochem., 118, 217–226, 2018.
Banerjee, S., Schlaeppi, K., and van der Heijden, M. G. A.: Keystone taxa as
drivers of microbiome structure and functioning, Nat. Rev. Microbiol., 16,
567–576, 2018.
Banerjee, S., Walder, F., Büchi, L., Meyer, M., Held, A. Y., Gattinger,
A., Keller, T., Charles, R., and van der Heijden, M. G. A.: Agricultural
intensification reduces microbial network complexity and the abundance of
keystone taxa in roots, ISME J., 13, 1722–1736, 2019.
Barberan, A., Bates, S. T., Casamayor, E. O., and Fierer, N.: Using network
analysis to explore co-occurrence patterns in soil microbial communities,
ISME J., 6, 343–351, 2012.
Barnes, A. D. Jochum, M., Mumme, S., Haneda, N. F., Farajallah, A., Widarto,
T. H., and Brose, U.: Consequences of tropical land use for multitrophic
biodiversity and ecosystem functioning, Nat. Commun., 5, 5351, https://doi.org/10.1038/ncomms6351, 2014.
Berry, D. and Widder, S.: Deciphering microbial interactions and detecting
keystone species with co-occurrence networks, Front. Microbiol., 5, 1–14,
2014.
Brinkmann, N., Schneider, D., Sahner, J., Ballauff, J., Edy, N., Barus, H.,
Irawan, B., Budi, S. W., Qaim, M., Danie, R., and Polle, A.: Intensive tropical
land use massively shifts soil fungal communities, Sci. Rep.-UK, 9, 3403, https://doi.org/10.1038/s41598-019-39829-4, 2019.
Cai, Z. Q., Zhang, Y. H., Yang, C., and Wang, S.: Land-use type strongly shapes
community composition, but not always diversity of soil microbes in tropical
China, Catena, 165, 369–380, 2018.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D.,
Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., and Gordon,
J. I.: QIIME allows analysis of high-throughput community sequencing data,
Nat. Methods, 7, 335–336, 2010.
Chen, J., Xu, H., He, D., Li, Y. D., Luo, T. S., Yang, H. G., and Lin, M. X.: Historical logging alters soil fungal community composition and
network in a tropical rainforest, Forest Ecol. Manage., 433, 228–239, 2019.
Coyte, K. Z., Schluter, J., and Foster, K. R.: The ecology of the microbiome:
networks, competition, and stability, Science, 350, 663–666, 2015.
De Vries, F. T. and Shade, A.: Controls on soil microbial community
stability under climate change, Front. Microbiol., 4, 265, https://doi.org/10.3389/fmicb.2013.00265, 2013.
De Vries, F. T., Griffiths, R. I., Mark, B., Craig, H., Girlanda, M., Gweon,
H. S., Hallin, S., Kaisermann, A., Keith, A. M., Kretzschmar, M., Lemanceau,
P., Lumini, E., Mason, K. E., Oliver, A., Ostle, N., Prosser, J. I., Thion,
C., Thomson, B., and Bardgett, R. D.: Soil bacterial networks are less stable
under drought than fungal networks, Nat. Commun., 9, 3033, https://doi.org/10.1038/s41467-018-05516-7, 2018.
Edgar, R. C.: UPARSE: Highly accurate OTU sequences from microbial amplicon
reads, Nat. Methods, 10, 996–998, 2013.
Egidi, E., Delgado-Baquerizo, M., Plett, J. M., Wang, J., Eldridge, D. J.,
Bardgett, R. D., Maestre, F. T., and Singh, B. K.: A few Ascomycota taxa dominate
soil fungal communities worldwide, Nat. Commun., 10, 2369, https://doi.org/10.1038/s41467-019-10373-z, 2019.
Francisco-Ortega, J., Wang, Z. S., Wang, F. G., Xing, F. W., Liu, H., Xu, H.,
Xu, W. X., Luo, Y. B., Song, X. Q., Gale, S., Boufford, D. E., Maunder, M., and
An, S. Q.: Seed plant endemism on Hainan Island: a framework for conservation
actions, Bot. Rev., 76, 346–376, 2010.
Fuhrman, J. A.: Microbial community structure and its functional
implications, Nature, 459, 193–199, 2009.
Geml, J., Timling, I., Robinson, C. H., Lennon, N., Nusbaum, H. C., Brochmann,
C., Noordeloos, M. E., and Taylor, D. L.: An arctic community of symbiotic
fungi assembled by dispersers: phylogenetic diversity of ectomycorrhizal
basidiomycetes in Svalbard based on soil and sporocarp DNA, J. Biogeogr.,
39, 74–88, 2012.
Gibson, L., Lee, T. M., Koh, L. P., Brook, B. W., Gardner, T. A., Barlow, J.,
Peres, C. A., Bradshaw, C. J. A., Laurance, W. F., Lovejoy, T. E., and Sodhi,
N. S.: Primary forests are irreplaceable for sustaining tropical biodiversity,
Nature, 478, 378–381, 2011.
Good, I. L.: The population frequencies of species and the estimation
of population parameters, Biometrika, 40, 237–264, 1953.
Jiao, S., Liu, Z. S., Lin, Y. B., Yang, J., Chen, W. M., and Wei, G. H.:
Bacterial communities in oil contaminated soils: biogeography and co-occurrence patterns, Soil Biol. Biochem., 98, 64–73, 2016.
Karimi, B., Maron, P. A., Chemidlin-Prevost Boure, N., Bernard, N., Gilbert,
D., and Ranjard, L.: Microbial diversity and ecological networks as
indicators of environmental quality, Environ. Chem. Lett., 15, 265–281, 2017.
Karimi, B., Dequiedt, S., Terrat, S., Jolivet, C., Arrouays, D.,
Wincker, P., Cruaud, C., Bispo, A., Prévost-Bouré, N. C., and Ranjard,
L.: Biogeography of soil bacterial networks along a gradient of cropping
intensity, Sci. Rep.-UK, 9, 3812, https://doi.org/10.1038/s41598-019-40422-y, 2019.
Kerfahi, D., Tripathi, B. M., Dong, K., Go, R., and Adams, J. M.: Rainforest
conversion to rubber plantation may not result in lower soil diversity of
bacteria fungi and nematodes, Microb. Ecol., 72, 359–371, 2016.
Kuperman, R. G., Siciliano, S. D., Römbke, J., and Oorts, K.: Deriving
site-specific soil clean-up values for metals and metalloids: rationale for
including protection of soil microbial processes, Integr. Environ. Assess., 10, 388–400, 2014.
Lan, G. Y., Li, Y. W., Wu, Z. X., and Xie, G. S.: Soil bacterial diversity impacted
by conversion of secondary forest to rubber or eucalyptus plantations – a
case study of Hainan Island, south China, Forest Sci., 63, 87–93, 2017a.
Lan, G. Y., Li, Y. W., Jatoi, M. T., Tan, Z. H., Wu, Z. X., and Xie, G. S.: Change
in soil microbial community compositions and diversity following the
conversion of tropical forest to rubber plantations in Xishuangbanan
southwest China, Trop. Conserv. Sci., 10, 1–14, 2017b.
Lan, G. Y., Li, Y., Wu, Z. X., and Xie, G. S.: Impact of tropical forest
conversion on soil bacterial diversity in tropical region of China, Eur. J.
Soil Biol., 83, 91–97, 2017c.
Lan, G. Y., Li, Y. W., Lesueur, D., Wu, Z. X., and Xie, G. S.: Seasonal changes
impact soil bacterial communities in a rubber plantation on Hainan Island
China, Sci. Total Environ., 626, 826–834, 2018.
Lan, G. Y., Wu, Z. X., Sun, R., Yang, C., Chen, B. Q., and Zhang, X. C.: Tropical
rainforest conversion into rubber plantations results in changes in soil
fungal composition, but underling mechanisms of community assembly remain
unchanged, Geoderma, 375, 114505, https://doi.org/10.1016/j.geoderma.2020.114505, 2020a.
Lan, G. Y., Wu, Z. X., Li, Y. W., and Chen, B. Q.: The drivers of soil bacterial
communities in rubber plantation at local and geographic scales, Arch.
Agron. Soil Sci., 66, 358–369, 2020b.
Lan, G. Y., Wu, Z. X., Sun, R., Yang, C., Chen, B. Q., and Zhang, X. C.: Forest
conversion changed the structure and functional process of tropical forest
soil microbiome, Land. Degrad. Dev., 32, 613–627, 2021.
Lopez, S., Rousset, F., Shaw, F. H., Ruth, G., Shaw, R. G., and Ophélie, R.:
Joint effects of inbreeding and local adaptation on the evolution of
genetic load after fragmentation, Conserv. Biol., 23, 1618–1627, 2009.
Louca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A., O'Connor,
M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., Crowe, S. A., Doebeli, M.,
and Parfrey, L. W.: Function and functional redundancy in microbial systems,
Nat. Ecol. Evol., 2, 936–943, 2018.
Ma, H., Zou, W., Yang, J., Hogan, J. A., and Chen, J.: Dominant tree species
shape soil microbial community via regulating assembly processes in planted
subtropical forests, Forests, 10, 978, https://doi.org/10.3390/f10110978, 2019.
Mills, L. S., Soulé, M. E., and Doak, D. F.: The keystone-species concept
in ecology and conservation, BioScience, 43, 219–224, 1993.
Morriën, E., Hannula, S. E., Snoek, L. B., Helmsing, N. R., Zweers, H.,
de Hollander, M., Soto, R. L., Bouffaud, M.-L., Buee, M., Dimmers, W.,
Duyts, H., Geisen, S., Girlanda, M., Griffiths, R. I., Jogensen, H.-B.,
Jensen, J., Plassart, P., Redecker, D., Schmelz, R. M., Schmidt, O.,
Thomson, B. C., Tisserant, E., Uroz, S., Winding, A., Bailey, M. J.,
Bonkowski, M., Faber, J. H., Martin, F., Lemanceau, P., de Boer, W., van
Veen, J. A., and van der Putten, W. H.: Soil networks become more connected and
take up more carbon as nature restoration progresses, Nat. Commun., 8,
14349, https://doi.org/10.1038/ncomms14349, 2017.
Mouquet, N., Gravel, D., Massol, F., and Calcagno, V.: Extending the concept
of keystone species to communities and ecosystems, Ecol. Lett., 16, 1–8, 2013.
Neutel, A. M., Heesterbeek, J. A. P., and de Ruiter, P. C.: Stability in real
food webs: weak links in long loops, Science, 296, 1120–1123, 2002.
Olesen, J. M., Bascompte, J., Dupont, Y. L., and Jordano, P.: The modularity of
pollination networks, P. Natl. Acad. Sci. USA, 104, 19891–19896, 2007.
Pagliai, M., Vignozzi, N., and Pellegrini, S.: Soil structure and the effect
of management practices, Soil Till. Res., 79, 131–143, 2004.
Philippot, L., Spor, A., Hénault, C., Bru, D., Bizouard, F.,
Jones, C. M., Sarr, A., and Maron, P. A.: Loss in microbial diversity affects
nitrogen cycling in soil Laurent, ISME J., 7, 1609–1619, 2013.
Power, M., Tilman, D., Estes, J., Menge, B., Bond, W., Mills, S., Daily, G.,
Castilla, J., Lubchenco, J., Paine, R., Power, M., Tilman, D., Estes, J.,
Menge, B., Bond, W., Mills, L., Daily, G., Castilla, J., Lubchenco, J., and
Paine, R.: Challenges in the quest for keystones, Bioscience, 46, 609–620,
1996.
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C.,
Nielsen, T., Pons, N., Levenez, F., and Yamada, T.: A human gut microbial gene
catalogue established by metagenomic sequencing, Nature, 464, 59–65, 2010.
Roger, G. and Amaral, L. A. N.: Functional cartography of complex metabolic
networks, Nature, 433, 895, https://doi.org/10.1038/nature03288, 2005.
Rooney, N., McCann, K., Gellner, G., and Moore, J. C.: Structural asymmetry
and the stability of diverse food webs, Nature, 442, 265–269, 2006.
Röttjers, L. and Faust, K.: From hairballs to hypotheses–biological
insights from microbial networks, FEMS Microbiol. Rev., 10, 1093, https://doi.org/10.1093/femsre/fuy030, 2018.
Sahner, J., Budi, S. W., Barus, H., Edy, N., Meyer, M., Corré, M. D.,
and Polle, A.: Degradation of root community traits as indicator for
transformation of tropical lowland rain forests into oil palm and rubber
plantations, PloS One, 10, e0138077, https://doi.org/10.1371/journal.pone.0138077, 2015.
Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan,
Z. E., Challis, C., Schretter, C. E., Rocha, S., Gradinaru, V., Chesselet,
M. F., Keshavarzian, A., Shannon, K. M., Krajmalnik-Brown, R.,
Wittung-Stafshede, P., Knight, R., and Mazmanian, S. K.: Gut microbiota
regulate motor deficits and neuroinflammation in a model of Parkinson's
disease, Cell, 167, 1469–1480, 2016.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M.,
Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., and Robinson,
C. J.: Introducing mothur: open-source, platform-independent,
community-supported software for describing and comparing microbial
communities, Appl. Environ. Microb., 75, 7537–7541, 2009.
Schneider, D., Engelhaupt, M., Allen, K., Kurniawan, S., Krashevska, V.,
Heinemann, M., and Scheu, S.: Impact of lowland rainforest transformation on
diversity and composition of soil prokaryotic communities in Sumatra
Indonesia, Front. Microbiol., 6, 296, https://doi.org/10.3389/fmicb.2015.01339, 2015.
Song, H., Singh, D., Tomlinson, K. W., Yang, X. D., Ogwu, M. C., Slik, J. W. F.,
and Adams, J. M.: Tropical forest conversion to rubber plantation in southwest
China results in lower fungal beta diversity and reduced network complexity,
FEMS Microbiol. Ecol., 95, fiz092, https://doi.org/10.1093/femsec/fiz092, 2019.
Stouffer, D. B. and Bascompte, J.: Compartmentalization increases food-web
persistence, P. Natl. Acad. Sci. USA, 108, 3648–3652, 2011.
Taniguchi, T., Kitajima, K., Douhan, G. W., Yamanaka, N., and Allen, M. F.: A
pulse of summer precipitation after the dry season triggers changes in
ectomycorrhizal formation, diversity, and community composition in a
Mediterranean forest in California, USA, Mycorrhiza, 28, 665–677, 2018.
Tripathi, B. M., Kim, M., Singh, D., Lee-Cruz, L., Lai-Hoe, A., Ainuddin, A.
N., and Adams, J. M.: Tropical soil bacterial communities in Malaysia: pH
dominates in the equatorial tropics too, Microb. Ecol., 64, 474–484, 2012.
Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E. E., and van der Heijden,
M. G. A.: Fungal-bacterial diversity and microbiome complexity predict
ecosystem functioning, Nat. Commun., 10, 4841, https://doi.org/10.1038/s41467-019-12798-y, 2019.
Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G.,
Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A.,
Apprill, A., and Knight, R.: Improved bacterial 16S rRNA gene (V4 and V4-5)
and fungal internal transcribed spacer marker gene primers for microbial
community surveys, mSystems, 1, e00009-15, https://doi.org/10.1128/mSystems.00009-15, 2016.
Yang, W., Zhang, D., Cai, X., Xia, L., Luo, Y. Q., Cheng, X., and An, S. Q.:
Significant alterations in soil fungal communities along a chronosequence of
spartina alterniflora invasion in a Chinese yellow sea coastal wetland, Sci. Total Environ.,
693, 133548, https://doi.org/10.1016/j.scitotenv.2019.07.354, 2019.
Zaller, J. G., Heigl, F., Ruess, L., and Grabmaier, A.: Glyphosate herbicide
affects belowground interactions between earthworms and symbiotic
mycorrhizal fungi in a model ecosystem, Sci. Rep., 4, 5634, https://doi.org/10.1038/srep05634, 2014.
Short summary
Forest conversion alters both bacterial and fungal soil networks: it reduces bacterial network complexity and enhances fungal network complexity. This is because forest conversion changes the soil pH and other soil properties, which alters the bacterial composition and subsequent network structure. Our study demonstrates the impact of forest conversion on soil network structure, which has important implications for ecosystem functions and the health of soil ecosystems in tropical regions.
Forest conversion alters both bacterial and fungal soil networks: it reduces bacterial network...