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Dufour OK, Hoffman E, Sleith RS, Katz LA, Weiner AKM, Sehein TR. Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing. Eur J Protistol 2024; 92:126049. [PMID: 38163403 PMCID: PMC11130782 DOI: 10.1016/j.ejop.2023.126049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.
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Affiliation(s)
- Olivia K Dufour
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Evie Hoffman
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Robin S Sleith
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, MA, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA.
| | - Agnes K M Weiner
- Smith College, Department of Biological Sciences, Northampton, MA, USA; NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor R Sehein
- Smith College, Department of Biological Sciences, Northampton, MA, USA
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Illuminating protist diversity in pitcher plants and bromeliad tanks. PLoS One 2022; 17:e0270913. [PMID: 35895712 PMCID: PMC9328516 DOI: 10.1371/journal.pone.0270913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and between host plant type. Across habitats, communities from tropical bromeliads grown in a single room of a greenhouse were nearly as heterogeneous as wild pitcher plants spread across hundreds of kilometers. At the scale of pitcher plants in a single bog, analyses of samples from three time points suggest that seasonality is a major driver of protist community structure, with variable spring communities transitioning to more homogeneous communities that resemble the surrounding habitat. Our results indicate that protist communities in phytotelmata are variable, likely due to stochastic founder events and colonization/competition dynamics, leading to tremendous heterogeneity in inquiline microeukaryotic communities.
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Molecular signature characters complement taxonomic diagnoses: a bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2022; 170:107433. [DOI: 10.1016/j.ympev.2022.107433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
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Ruggiero A, Grattepanche JD, Weiner AKM, Katz LA. High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon-specific Primers. J Eukaryot Microbiol 2020; 67:450-462. [PMID: 32145128 DOI: 10.1111/jeu.12794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2-10, 10-35, 35-100, and 100-300 μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized by DNA (i.e. active + quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life-history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.
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Affiliation(s)
- Alistaire Ruggiero
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Jean-David Grattepanche
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Agnes K M Weiner
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Laura A Katz
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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Grattepanche J, Santoferrara LF, McManus GB, Katz LA. Unexpected biodiversity of ciliates in marine samples from below the photic zone. Mol Ecol 2016; 25:3987-4000. [DOI: 10.1111/mec.13745] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - George B. McManus
- Department of Marine Sciences University of Connecticut Groton CT 06340 USA
| | - Laura A. Katz
- Department of Biological Sciences Smith College Northampton MA 01063 USA
- Program in Organismic and Evolutionary Biology University of Massachusetts Amherst MA 01003 USA
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Uthup TK, Rajamani A, Ravindran M, Saha T. Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:720-728. [PMID: 26787454 DOI: 10.1111/plb.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
Hydroxy-methylglutaryl coenzyme-A synthase (HMGS) is a rate-limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non-coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three-dimensional structural studies highlighting the structural positioning of non-synonymous SNPs from different HMGS haplotypes revealed that the ligand-binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants.
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Affiliation(s)
- T K Uthup
- Genome Analysis Laboratory, Rubber Research Institute of India, Kottayam, Kerala, India
| | - A Rajamani
- Genome Analysis Laboratory, Rubber Research Institute of India, Kottayam, Kerala, India
| | - M Ravindran
- Genome Analysis Laboratory, Rubber Research Institute of India, Kottayam, Kerala, India
| | - T Saha
- Genome Analysis Laboratory, Rubber Research Institute of India, Kottayam, Kerala, India
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Jung JH, Park KM, Yang EJ, Joo HM, Jeon M, Kang SH, Choi HG, Park MH, Min GS, Kim S. Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing. Anim Cells Syst (Seoul) 2015. [DOI: 10.1080/19768354.2015.1082931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses. Appl Microbiol Biotechnol 2015; 99:2513-21. [DOI: 10.1007/s00253-015-6427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
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Kim SJ, Lee KY, Ju SJ. Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding. Mol Ecol Resour 2013; 13:781-7. [PMID: 23663201 DOI: 10.1111/1755-0998.12119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 11/30/2022]
Abstract
Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.
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Affiliation(s)
- Se-Joo Kim
- Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science & Technology, Gyeonggi-do, 426-744, Korea
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