Habitat filters mediate successional trajectories in bacterial communities associated with the striped shore crab
The relative importance of stochastic- and niche-based processes shifts during successional time and across different types of habitats. Microbial biofilms are known to undergo such successional shifts. However, little is known about the interaction between these successional trajectories and habitat filters. Harsh habitat filters could affect biofilm successional trajectories by strengthening niche-based processes and weakening stochastic processes. We used mesocosms to track successional trajectories in bacterial communities associated with the striped shore crab (Pachygrapsus transversus). We followed replicated microbial communities under strong and weak habitat filters associated with the crab’s gut and carapace. For bacteria, colonization of the crab’s gut is constrained by strong chemical and physical filtering, while the carapace remains relatively open for colonization. Consistent with successional models of bacterial biofilms, carapace microbial communities initially converged in community composition at day 8 and diverged thereafter. We expected gut microbial communities to deviate from the trajectory in the carapace and converge towards a subset of tolerant species. Instead, bacterial communities in the gut exhibited low richness, unchanging similarity in composition and turnover in species identities throughout the duration of our study. These habitat filter effects were linked with weak species interactions and low influence from colonization in the gut. If these findings are representative of differences in filter strength in a continuum of successional trajectories, habitat filters may provide basis for predictions that link successional models and habitat types.
KeywordsHabitat filters Succession Community assembly Community structure Colonization
We would like to thank Deana Erdner for her guidance and generous sharing of laboratory space. Mathew Leibold and Casey terHorst provided excellent comments to early drafts. Finally, we thank Kathryn Thompson for her participation in crab collection.
Author contribution statement
CCG and PM conceived and designed the experiment. CCG conducted the experiment, and analyzed the data. CCG and PM wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Andrews S (2010) FastQC: a quality control tool for high throughput sequence dataGoogle Scholar
- Brorcard D, Legendre P, Drapeau P (1992) Partialling out the spatial component of ecological variation. Ecology 73:511–525Google Scholar
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pẽa AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing dataGoogle Scholar
- Cuellar-Gempeler C, Leibold MA (2019) Key colonist pools and habitat filters mediate the composition of fiddler crab-associated bacterial communities. Ecol pressGoogle Scholar
- Dilhari A, Sampath A, Gunasekara C, Fernando N, Weerasekara D, Sissons C, McBain A, Weerasekera M (2017) Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method. AMB Express 7:179PubMedPubMedCentralCrossRefGoogle Scholar
- Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6:65–70Google Scholar
- Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, PrincetonGoogle Scholar
- Kraft NJB, Comita LS, Chase JM, Sanders NJ, Swenson NG, Crist TO, Stegen JC, Vellend M, Boyle B, Anderson MJ, Cornell HV, Davies KF, Freestone AL, Inouye BD, Harrison SP, Myers JA (2011) Disentangling the drivers of beta diversity along latitudinal and elevational gradients. Science 333:1755–1758PubMedCrossRefGoogle Scholar
- Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, Boehm F, Caporaso NE, Cornelis MC, Edenberg HJ, Gabriel SB, Harris EL, Hu FB, Jacobs KB, Kraft P, Landi MT, Lumley T, Manolio TA, McHugh C, Painter I, Paschall J, Rice JP, Rice KM, Zheng XW, Weir BS, Investigators G (2010) Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol 34:591–602PubMedPubMedCentralCrossRefGoogle Scholar
- McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS OneGoogle Scholar
- Mouquet N, Loreau M (2003) Community patterns in source-sink metacommunities. Am NatGoogle Scholar
- Oksanen J, Blanchet G, Kindt R, Legendre P, Minchin P, O’Hara GL, Simpson GL, Solymos P, Stevens MHH, Wagner H (2017) Vegan: community ecology packageGoogle Scholar
- Oksanen AJ, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, Minchin PR, Hara RBO, Simpson GL, Solymos P, Szoecs SE, Wagner H (2018) Vegan: community ecology package. https://github.com/vegandevs/vegan
- Rathbun MJ (1918) The grapsoid crabs of America. Bull US Natl Museum 97:1–461Google Scholar
- Rognes T, Flouri T, Nichols B, Quince C, Frédéric M (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJGoogle Scholar
- Vavrek MJ (2011) fossil: palaeoecological and palaeogeographical analysis tools. Palaeontol Electron 14:1–16Google Scholar
- Wang W, Wu XG, Liu ZJ, Zheng HJ, Cheng YX (2014) Insights into hepatopancreatic functions for nutrition metabolism and ovarian development in the crab Portunus trituberculatus: gene discovery in the comparative transcriptome of different hepatopancreas stages. Plos One 9:e84921PubMedPubMedCentralCrossRefGoogle Scholar
- Wright JP, Fridley JD (2010) Biogeographic synthesis of secondary succession rates in eastern North America. J Biogeogr 37:1584–1596Google Scholar