Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109997/1/lno20105562381.pd

Defining DNA-based operational taxonomic units for microbial-eukaryote ecology

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 75 (2009): 5797-5808, doi:10.1128/AEM.00298-09.DNA sequence information has been increasingly used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, the autecology of ecologically relevant species, and the identification and enumeration of species of interest to human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is partly a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes, and partly the problematic nature and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximate species-level distinctions. The approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small subunit ribosomal RNA (18S) gene sequences and partial gene sequences obtained from GenBank for morphologically described protistan species. The program was tested using environmental 18S data sets from two oceanic ecosystems. A total of 388 operational taxonomic units were observed among 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific.Support for this manuscript was provided by National Science Foundation grants MCB-0732066, MCB-0703159 and OCE-0550829 and a grant from the Gordon and Betty Moore Foundation

Processes That Contribute to Decreased Dimethyl Sulfide Production in Response to Ocean Acidification in Subtropical Waters

Long-term time series data show that ocean acidification is occurring in the subtropical oceans. As a component of an in situ mesocosm experiment carried out offGran Canaria in the subtropical North Atlantic, we examined the influence of ocean acidification on the net production of dimethylsulfide (DMS). Over 23 days under oligotrophic conditions, time-integrated DMS concentrations showed an inverse relationship of -0.21 ± 0.02 nmol DMS nmol-1 H+ across the gradient of H+ concentration of 8.8-23.3 nmol l-1, equivalent to a range of pCO2 of 400-1,252 atm. Proportionally similar decreases in the concentrations of both dissolved and particulate dimethylsulfoniopropionate (DMSP) were observed in relation to increasing H+ concentration between the mesocosms. The reduced net production of DMSP with increased acidity appeared to result from a decrease in abundance of a DMSP-rich nanophytoplankton population. A 35S-DMSP tracer approach was used to determine rates of dissolved DMSP catabolism, including DMS production, across the mesocosm treatments. Over a phase of increasing DMS concentrations during the experiment, the specific rates of DMS production were significantly reduced at elevated H+ concentration. These rates were closely correlated to the rates of net DMS production indicating that transformation of dissolved DMSP to DMS by bacteria was a major component of DMS production. It was not possible to resolve whether catabolism of DMSP was directly influenced by H+ concentrations or was an indirect response in the bacterial community composition associated with reduced DMSP availability. There is a pressing need to understand how subtropical planktonic communities respond to the predicted gradual prolonged ocean acidification, as alterations in the emission of DMS from the vast subtropical oceans could influence atmospheric chemistry and potentially climate, over a large proportion of the Earth's surface

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible ‘keystone’ species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.Keywords: Operational taxonomic units, Protistan diversity, Species richness, Ciliate environmental diversit

Concentrations of DMS, DMSPp, DMSPd, & DMSOd in relation to ocean acidification [H+] during the KOSMOS 2014 mesocosm experiment off Gran Canaria

Dataset: KOSMOS14 DMSPO ConcentrationsConcentrations of DMS, DMSPp, DMSPd, & DMSOd in relation to ocean acidification [H+] during the KOSMOS 2014 mesocosm experiment off Gran Canaria. The full experiment took place from 23rd September to 25th November 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/769302NSF Division of Ocean Sciences (NSF OCE) OCE-131613

A qPCR-Based Survey of Haplosporidium nelsoni and Perkinsus spp. in the Eastern Oyster, Crassostrea virginica in Maine, USA

Eastern oyster (Crassostrea virginica) aquaculture is increasingly playing a significant role in the state of Maine’s (USA) coastal economy. Here, we conducted a qPCR-based survey for Haplosporidium nelsoni, Perkinsus marinus, and Perkinsus chesapeaki in C. virginica (n = 1440) from six Maine sites during the summer–fall of 2016 and 2017. In the absence of reported die-offs, our results indicated the continued presence of the three protozoan parasites in the six sites. The highest H. nelsoni qPCR-prevalence corresponded to Jack’s Point and Prentiss Island ( x ¯ = 40 and 48% respectively), both located in the Damariscotta River Estuary. Jack’s Point, Prentiss Island, New Meadows River, and Weskeag River recorded the highest qPCR-prevalence for P. marinus (32–39%). While the P. marinus qPCR-prevalence differed slightly for the years 2016 and 2017, P. chesapeaki qPCR-prevalence in 2016 was markedly lower than 2017 (<20% at all sites versus >60% at all sites for each of the years, respectively). Mean qPCR-prevalence values for P. chesapeaki over the two-year study were ≥40% for samples from Jack’s Point (49%), Prentiss Island (44%), and New Meadows River (40%). This study highlights that large and sustained surveys for parasitic diseases are fundamental for decision making toward the management of the shellfish aquaculture industry, especially for having a baseline in the case that die-offs occur

Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments

Little is known about protists at deep-sea hydrothermal vents. The vent sites at Guaymas Basin in the Gulf of California are characterized by dense mats of filamentous pigmented or nonpigmented Beggiatoa that serve as markers of subsurface thermochemical gradients. We constructed 18S rRNA libraries to investigate ciliate assemblages in Beggiatoa mats and from bare sediments at the Guaymas vent site. Results indicated a high diversity of ciliates, with 156 operational taxonomic units identified in 548 sequences. Comparison between mat environments demonstrated that ciliate and bacterial assemblages from pigmented mats, nonpigmented mats, and bare sediments were significantly different and highly correlated with bacterial assemblages. Neither bacterial nor ciliate assemblages were correlated with environmental factors. The most abundant ciliates at Guaymas were more likely to be represented in clone libraries from other hydrothermal, deep-sea, and/or anoxic or microaerophilic environments, supporting the hypothesis that these ciliate species are broadly distributed. The orange mat environment included a higher proportion of ciliate sequences that were more similar to those from other environmental studies than to cultured ciliate species, whereas clone libraries from bare sediments included sequences that were the most highly divergent from all other sequences and may represent species that are endemic to Guaymas