Marine Invasions Research

Principal Investigator

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Biological invasions - the establishment of species beyond their historical range - are a major force of ecological and evolutionary change. Our lab aims to understand the patterns, processes, and consequences of invasions in marine ecosystems on local to global scales.  We have laboratories and staff on both coasts of North America, on Chesapeake Bay and San Francisco Bay (Tiburon Lab).  These bays are focal points for our long-term, intensive research, which spans Pacific and Atlantic shorelines of the Americas --- from polar to tropical latitudes. 

Most marine invasions result from human-mediated species transfers, which are often associated with commercial and recreational vessels. A major component of our research examines shipping, transportation, and trade dynamics for the United States with the National Ballast Information Clearinghouse (NBIC), a joint program with the U.S. Coast Guard that is based at SERC.  NBIC tracks the status and trends of ballast water delivery and management for the Nation.

Our research encompasses a wide range of projects, exploring the ecology and management of coastal marine ecosystems.  We focus primarily on invasion dynamics but also examine species interactions of both native and non-native species. Overall, we seek to: (1) characterize patterns of marine invasion across space, time, and taxonomic groups; (2) develop a mechanistic understanding of the processes that drive observed patterns; (3) advance predictive capability about the establishment, spread, and impacts of non-native species in marine ecosystems; (4) evaluate the efficacy of management strategies to limit the establishment and impact of invaders; and (5) understand the roles of species interactions, including predator-prey and host-parasite relationships, in marine communities. 

Further details on the various dimensions of our work are available below. 

Ojaveer, H, Galil, B.S., Carlton, J.T., Alleway, H., Goulletquer, P., Lehtinemi, M., Marchini, A., Miller, A.W., Occhipinti-Ambrogi, A., Peharda, M., Ruiz, G.M., Williams, S.L., and Zaiko, A. 2018.  Historical baselines in marine bioinvasions: Implications for policy and management. PLOS One https://doi.org/10.1371/journal.pone.0202383 (online: August 16, 2018)

Heller, P., Casaletto, J., Ruiz, G., and Geller, J. 2018. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Scientific Data doi: 10.1038/sdata.2018.156 (Online August 7, 2018)

Darling, J., Martinson, J., Gong, Y., Okum, S., Pilgrim, E., Lohan, K., Carney, K.J., and Ruiz, G. 2018. Ballast water exchange and invasion risk posed by intra-coastal vessel traffic: An evaluation using high throughput sequencing. Environmental Science & Technology 
DOI: 10.1021/acs.est.8b02108 (Online July 30, 2018)

Zabin, C. J.Davidson, I.C., Holzer, K.K., Smith, G., Ashton, G.V., Tamburri, M.N., and Ruiz, G.M. 2018. How will vessels be inspected to meet emerging biofouling regulations for the prevention of marine invasions? Management of Biological Invasions (9). (Online: June, 18 2018)

Keppel, E., Tovar-Hernández, M.A., Ruiz, G.M. 2018. New records of the non-indigenous species Branchiomma bairdi and B. conspersum (Polychaeta: Sabellidae) on the Pacific coast of North America. BioInvasions Records (7) (online June 7, 2018)


Abstracts

August 16, 2018

Ojaveer, H, Galil, B.S., Carlton, J.T., Alleway, H., Goulletquer, P., Lehtinemi, M., Marchini, A., Miller, A.W., Occhipinti-Ambrogi, A., Peharda, M., Ruiz, G.M., Williams, S.L., and Zaiko, A. 2018.  Historical baselines in marine bioinvasions: Implications for policy and management. Plos One https://doi.org/10.1371/journal.pone.0202383

The human-mediated introduction of marine non-indigenous species is a centuries- if not millennia-old phenomenon, but was only recently acknowledged as a potent driver of change in the sea. We provide a synopsis of key historical milestones for marine bioinvasions, including timelines of (a) discovery and understanding of the invasion process, focusing on transfer mechanisms and outcomes, (b) methodologies used for detection and monitoring, (c) approaches to ecological impacts research, and (d) management and policy responses. Early (until the mid-1900s) marine bioinvasions were given little attention, and in a number of cases actively and routinely facilitated. Beginning in the second half of the 20th century, several conspicuous non-indigenous species outbreaks with strong environmental, economic, and public health impacts raised widespread concerns and initiated shifts in public and scientific perceptions. These high-profile invasions led to policy documents and strategies to reduce the introduction and spread of non-indigenous species, although with significant time lags and limited success and focused on only a subset of transfer mechanisms. Integrated, multi-vector management within an ecosystem-based marine management context is urgently needed to address the complex interactions of natural and human pressures that drive invasions in marine ecosystems.

August 7, 2018

Heller, P., Casaletto, J., Ruiz, G., and Geller, J. 2018. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Scientific Data doi: 10.1038/sdata.2018.156

The Cytochrome C Oxidase subunit I gene (“COI”) is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD’s submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive. Midori, derived from GenBank, has more sequences but less stringent standards than BOLD, resulting in higher error rates. To address the need for a comprehensive and accurate COI database, we adapted the ARBitrator algorithm, which classifies based only on sequence properties and has successfully auto-curated bacterial genes mined from GenBank. The adapted algorithm, which we call CO-ARBitrator, built a database of over a million metazoan COI sequences. Sensitivity and specificity are significantly higher than Midori. Specificity is comparable to what BOLD achieves with data quality prerequisites. Results and software are publicly available.

July 30, 2018

Darling, J., Martinson, J., Gong, Y., Okum, S., Pilgrim, E., Lohan, K., Carney, K.J., and Ruiz, G. 2018. Ballast water exchange and invasion risk posed by intra-coastal vessel traffic: An evaluation using high throughput sequencing. Environmental Science & Technology 
DOI: 10.1021/acs.est.8b02108

Ballast water remains a potent vector of non-native aquatic species introductions, despite increased global efforts to reduce risk of ballast water mediated invasions. This is particularly true of intra-coastal vessel traffic, whose characteristics may limit the feasibility and efficacy of management through ballast water exchange (BWE). Here we utilize High Throughput Sequencing (HTS) to assess biological communities associated with ballast water being delivered to Valdez, Alaska from multiple source ports along the Pacific Coast of the United States. Our analyses indicate that BWE has a significant but modest effect on ballast water assemblages. Although overall richness was not reduced with exchange, we detected losses of some common benthic coastal taxa (e.g. decapods, mollusks, bryozoans, cnidaria) and gains of open ocean taxa (e.g., certain copepods, diatoms, and dinoflagellates), including some potentially toxic species. HTS-based metabarcoding identified significantly differentiated biodiversity signatures from individual source ports; this signal persisted, though weakened, in vessels undergoing BWE, indicating incomplete faunal turnover associated with management. Our analysis also enabled identification of taxa that may be of particular concern if established in Alaskan waters. While these results reveal a clear effect of BWE on diversity in intra-coastal transit, they also indicate continued introduction risk of non-native and harmful taxa.

June 18, 2018

Zabin, C. J.Davidson, I.C., Holzer, K.K., Smith, G., Ashton, G.V., Tamburri, M.N., and Ruiz, G.M. 2018. How will vessels be inspected to meet emerging biofouling regulations for the prevention of marine invasions? Management of Biological Invasions (9).

International and national guidelines and regulations to limit the inadvertent transfer of non-native species on the submerged surfaces of vessels and mobile infrastructure are progressing. However, methods to assess compliance must be developed to assist both regulators and industry. While there is a history of biofouling inspections in maritime industries, including commercial shipping and infrastructure, such surveys are tailored for vessel safety and performance rather than being driven by biosecurity purposes. Thus, these inspections are likely inadequate for confirming compliance with biosecurity regulations. To determine regulatory compliance, agencies will likely rely on a combination of risk profiling, assessment of documentation of biofouling management, archival data and images, and real-time in-water surveys made by divers or remotely operated vehicles (ROVs) specific to biosecurity regulations. Divers may exceed ROVs at finding organisms in recesses and other topographically complex areas, and when regulations require confirmation of species identity or viability. In contrast, ROVs may be well suited for regulations that establish upper thresholds on biofouling levels with little concern for organism identity or condition. Several factors will inform how a survey is conducted, including cost, the type of data required by regulations, environmental conditions, safety, and logistics. Survey designs and requirements should be transparent to manage industry’s expectations of border procedures, to increase the efficiency with which industry and agencies manage biofouling and potentially align the evaluation of best practices in hull and niche area maintenance across jurisdictions.

June 7, 2018

Keppel, E., Tovar-Hernández, M.A., Ruiz, G.M. 2018. New records of the non-indigenous species Branchiomma bairdi and B. conspersum (Polychaeta: Sabellidae) on the Pacific coast of North America. BioInvasions Records (7)

Among Sabellidae (polychaetes commonly found in hard substrate fouling communities), the genus Branchiomma Kölliker is a species-rich group with an expanding global history of invasions. In this paper, we report the first new records of Branchiomma bairdi along the Californian and Hawaiian coasts. Moreover, we confirm the first recorded introduction and range extension of Branchiomma conspersum. Branchiomma conspersum is originally from the Caribbean Sea and is a new non–indigenous species on the Pacific side of Panama and is also present in Hawaii and Australia. 

Species distributions are at the core of all ecological and evolutionary processes. Despite recognition that accelerating invasions are radically changing fundamental ecological processes, we currently lack the data for a broad scale understanding of these  patterns, emergent properties, and practical implications across both spatial and temporal scales. We are collecting quality occurrence data and using these data to understand patterns and mechanisms of invasion, and making these data publicly available for broader application by the public.

Our Projects

The impacts of introduced species pose significant challenges for conservation and restoration because they undermine a desired outcome for target species or habitats. In addition, some invasions impose significant economic costs through loss of agriculture, forestry, and fisheries products, and others, including mosquito-borne viruses and toxic algal blooms, have severe human health effects. Detailed analysis of several high-profile species invasions have highlighted the types and potential magnitude of invasion impacts that exist, however, the effect of most non-native species and the full scope of impacts from invasions remains poorly understood. To address this gap, we use a variety of approaches to characterize and test the ecological, evolutionary, and social effects of non-native species across diverse ecosystems.  This work advances understanding of how the Earth’s ecosystems function and also serve to inform resource management and conservation strategies.

Our Projects

Biological invasions provide opportunities to examine how species and ecosystems respond to new arrivals, and how species adapt to new environmental conditions. These types of “natural experiments” provide new insights into many biological processes, especially early in the colonization process, that are not possible with native communities.  We examine invasion ecology at the population, community, and ecosystem level across a diverse range of habitats and organisms, both to advance basic science and inform management and conservation strategies.

Our Projects

Managing biological invasions is a worldwide endeavor that aims to (a) prevent the human-caused spread of species, (b) control and remove unwanted species, and (c) reduce negative impacts to society and the environment. We are evaluating the efficacy and consequences of invasion management strategies and policies in coastal estuaries and marine systems.  Our work is often done in collaboration with local, state, federal and international partners and used actively to inform current management and policy decisions.

Our Projects

We study the dynamic interactions between society, trade, transport, and species in a variety of ways. These include modeling transport networks and biotic exchange, evaluating business model forecasts and their effects on trade routes and species distributions, and assessments of organism transfers across major corridors between oceans and continents.

Our Projects

Understanding how modes of human transportation affect the environment, and biological invasions in particular, is complicated and involves many components including both human and natural history. Human history because most invasions result from human-aided species transfers and invasion patterns often reflect human movements and transportation systems. Natural history because species identifications and their life history characteristics are paramount to knowing which species are non-native and how they have likely been introduced. We work to address these complexities and strive to understand the dynamics of species transport in marine systems. 

Our Projects

Balanced predation and competition are key to the health of any ecosystem. We are examining predation and competition rates in several environments including in the Rhode River near SERC where we study native species in nearshore environments and in introduced fouling communities on the Atlantic and Pacific coasts.  

Our Projects

Communities are constantly being shaped by human activities, activates that can affect hydrology, climate, chemical inputs, species richness (number of species that make up the community), as well as habitat quantity and quality. Our research focuses on how biological invasions change the marine and estuarine communities they invade and how recipient communities protect themselves from invasion. The following highlights a few of our recent projects exploring community changes resulting from nonnative species introductions.

Our Projects

Laravel tunicates

Propagule Pressure in Marine Habitats

We are examining the complex, dynamic interactions between parasites and their hosts, including both the evolutionary and ecological mechanisms that influence these interactions. Our research includes a wide variety of hosts (e.g., seagrasses, bivalves, crustaceans) and parasites (e.g., protists, bacteria, crustaceans).