The BUilding Infrastructure Leading to Diversity (BUILD) undergraduate research training program is funded by the National Institutes of Health (NIH) to strengthen the pipeline for underrepresented students through graduate school and into health-related research careers in the biomedical and behavioral sciences. This study evaluates the impact of BUILD participation at a Minority-Serving Institution in Southern California on graduate school outcomes up to 6 years post-graduation including doctoral program enrollment and degree attainment using a quasi-experimental design. BUILD students were compared to a propensity score matched non-BUILD group using logistic regression. Results showed BUILD students enrolled in Ph.D. programs and attained Ph.Ds. at a higher rate compared to matched peers. Findings indicate BUILD met a pivotal program objective to increase doctoral degree attainment imperative for health-related research careers in biomedical and behavioral sciences. Furthermore, results support the added value of undergraduate research programs for students from underrepresented backgrounds.

Engaging students in research is a high impact practice known to increase underrepresented students' persistence in Science, Technology, Engineering, and Mathematics (STEM) fields and improve their graduation rates. For broad impact, research infusion can be implemented through careful redesign of courses or through the adoption of research modules to supplement class instruction and existing student training programs. In this paper, we present data on a program for the design and implementation of research-infused curricula in major courses across a variety of STEM and related disciplines. Specifically, the Research Across the Curriculum program's goal was to have faculty engage in a redesign of a class to exemplify how specific disciplines engage in research. Fourteen courses were included in the present analysis, and the redesigned components were implemented in the form of interactive activities for in-person or online learning. Overall, the redesigned courses had a large impact on student's perceptions of gains in research skills. Students reported moderate to good gains in understanding the relevance of research in their discipline and skills important to research like problem solving, understanding research papers, and interpreting research results. The modality of the course (online vs. face-to-face) had little impact. Thus, research-focused activities intentionally embedded in courses strengthen the research foundation of students and should be encouraged as a high-impact practice.

Engaging undergraduates in research is a high impact practice shown to increase underrepresented students' persistence in Science, Technology, Engineering, and Mathematics (STEM) fields and entry into research careers. The California State University Long Beach (CSULB) BUilding Infrastructure Leading to Diversity (BUILD) Scholars Program is a 2-year, upper-division research training program. Although similar research training programs exist, most admit relatively few students a year, primarily from the natural sciences. The BUILD award from the National Institutes of Health (NIH) allowed us to broaden research training to a wider range of health-related disciplines across four different colleges to have more even representation across the behavioral and biomedical science disciplines. Our Scholars Program builds upon best practices of programmatic mentoring, assets-based and cohort-based training, financial and educational support, and intensive research training by faculty in the students' disciplines. In this paper, we present the outcomes and evaluation of our training program with data from the first phase of the BUILD award (2015-2019). Findings demonstrate that our Scholars Program was effective at recruiting and retaining underrepresented students from a broad range of disciplines. Moreover, our trainees demonstrated a high level of research engagement through off-campus summer research experiences, conference presentations, and publications. The intensive training in the Scholars Program also yielded high graduate school acceptance rates for our trainees. Most importantly, our findings show that it is possible to broaden an intensive undergraduate research training program that is similarly effective for trainees across behavioral and biomedical disciplines, underrepresented minority status, and gender. While we highlight several elements of our training program, we emphasize these components likely work together interactively, and institutions wanting to establish a similar training program need to ensure sufficient resources for its successful implementation.

Critical to the environmental sustainability of hard rock mining is the reclamation of disturbed lands following mine closure through revegetation. Improved understanding of associations between above- and belowground processes that characterize successful plant establishment is critical to the implementation of more efficient revegetation strategies for nutrient-poor mine waste materials. The specific objective of this five-year temporal study was to identify progressive biotic and abiotic indicators of primary soil development on mine waste rock (WR) on a slope hydroseeded with native plant species and to quantify comparative effects of plant lifeform on soil development. Aboveground plant diversity and belowground substrate properties were measured annually at 67 m intervals along transects following the slope contour. Seeded WR was compared to unseeded WR and the adjacent native ecosystem. A temporal increase in WR microbial biomass was observed in seeded WR relative to unseeded areas. Microbial community analysis found the unseeded WR to be defined by oligotrophic microbes, whereas targeted grass and shrub root zones samples demonstrated significant increases in specific cellulose and lignin degrading and N-cycling phylotypes. More extensive chemical and biological fertility development was observed in shrub root zones relative to grass. Ten chemical and biological indicators increased significantly in shrub WR relative to unseeded WR, whereas grass WR was only enriched in bacterial 16S rRNA gene copy number/g substrate and bacterial/archaeal and fungal diversity. In addition, the shrub root zone had significantly higher nitrogen-cycling potential than grass root zones or unseeded WR. Thus, both grasses and shrubs improve belowground WR development; however, shrub establishment had greater fertility outcomes. Concurrent belowground fertility development is critical to sustainable plant establishment. Coupled evaluation of above- and belowground metrics provides an improved quantitative assessment of revegetation progress and a valuable tool to guide management decisions.

There is a broad need to support the early educational trajectories of underrepresented students pursuing behavioral and biomedical research, particularly at large, comprehensive institutions. The Building Infrastructure Leading to Diversity (BUILD) initiative at California State University Long Beach (CSULB) created an Associates Program designed to provide undergraduates with early exposure to research and foster a sense of belonging and interest in a research career during their sophomore year. Our Associates Program had high retention rates (> 90%) and served as a pathway to other research opportunities on campus, with over half of the students entering an intensive, upper-division research training program at CSULB upon completion. Analysis of evaluation data gathered at multiple points throughout the training program provided preliminary evidence that our early intervention program resulted in student trainees' growth in a number of key areas, including their sense of belong to the BUILD Program, interests in science and research, and understanding of what research entails and of the skills necessary for conducting research (e.g., scientific writing, oral presentation, data analysis). More importantly, comparisons of the students who continued on to an upper-division research training program to those who did not continue revealed that students who continued reported generally higher levels of science/research interests regardless of the time points of the survey, and a greater increase in their perception of gains made in some areas of research during the second half of the training program. Lastly, our results also showed that the Associates Program is similarly effective for trainees across behavioral and biomedical disciplines, underrepresented minority status, and gender. Based on these findings, we conclude that an early intervention program for undergraduate students results in development of research skills for students exploring research and serves as an effective pipeline for diverse students into more intensive upper-division training programs.

Juvenile common thresher sharks ( Alopias vulpinus) have been recently stranding along the California coastline. Using Illumina sequencing of the bacterial 16S rRNA gene along with necropsy, cytological, bacteriological, and histological techniques, we screened microbial communities and described lesions characterizing affected sharks with the purpose of identifying potential pathogen sources and pathologic processes. Histopathological assessment of moribund sharks revealed severe meningoencephalitis, as previously described in stranded salmon sharks ( Lamna ditropis), along with inflammation of the inner ear and subcutaneous tissues surrounding the endolymphatic ducts. Furthermore, inflamed areas were characterized by the prevalence of Carnobacterium maltaromaticum, suggesting this bacterium as a potential pathogen that gains access to the inner ear through the endolymphatic ducts, with subsequent spread into the brain. The absence or low abundance of this bacterium in the spiral valve in both healthy and infected sharks suggests that Carnobacterium is not a commensal member of their digestive communities and the spiral valve is unlikely to be the source of the pathogen. Furthermore, phylogenetic analysis suggests that C. maltaromaticum strains isolated from diseased sharks have minimal genetic variation and differ from other strains originating from food or diseased teleosts. While a C. maltaromaticum–like organism has previously been associated with meningoencephalitis in salmon shark strandings, this is the first study to report common thresher shark strandings associated with C. maltaromaticum, involving the endolymphatic ducts as portals of entry to the brain.

Engaging students in research is a high impact practice that improves student retention and persistence in behavioral and biomedical sciences and engineering. The California State University Long Beach (CSULB) Building Infrastructure Leading to Diversity (BUILD) Program offers an intensive research training experience to undergraduate students from a wide range of health-related disciplines. The goal of this program is to provide students with research skills, psychosocial resources, and graduate school application guidance that will make them competitive for Ph.D. programs. With the COVID-19 pandemic forcing the campus closure of many universities, including CSULB, our student training had to transition from in-person training to online training. This paper discusses the development and implementation of a series of eight online modules for guiding students through the application process for summer research experiences and graduate schools. Overall, the BUILD trainees were positive about the online modules. Specifically, they indicated that the modules were useful, informative, easy to access/use, good use of their time, and a good supplemental activity to their learning community activities. Most trainees indicated that they preferred the modules to be implemented in a hybrid format, where the students can view the modules on their own first and then have an opportunity to engage in in-person/synchronous online discussions.

Southern California coastal wetlands are heavily impacted by urbanization and are under increased inundation stress due to sea level rise (SLR). This study evaluated the impacts of inundation on decomposition rates and sediment decomposer communities (invertebrates, fungi, and bacteria) by manipulating inundation using a marsh organ. Under increased inundation, invertebrate diversity decreased, and plant litter decomposition was reduced by excluding fungi and invertebrates from substrates using litter bags, indicating that all three decomposer guilds are important. This study showed significant impacts of increased inundation on bacterial, fungal and invertebrate community structure and diversity, yet only modest effects on sulfate reduction and decomposition rates, suggesting a degree of resilience or functional redundancy in the decomposer community. While the marsh organ successfully simulated increased inundation, it also created experimental ‘bottle effects’ that may have obscured inundation treatment effects and altered communities from the natural marsh. In our study, invertebrates were most sensitive to inundation, while bacteria appeared to be more resistant. This has implications for how decomposition and associated biogeochemical and ecological processes might change in the face of increased inundation due to SLR and suggests that marsh organs may be less suitable for investigating microbial communities compared with plants.

Coliforms are important bacterial contamination indicators in recreational waters. Little is known about the antibiotic resistance of coliforms from Southern California beaches. This study examined the numbers of coliforms as well as the incidence of antibiotic-resistant coliforms in beaches with restricted and non-restricted wave action by sampling from the shores of both types of beaches following dry and wet weather. Total coliforms were selected by membrane filtration onto mEndo agar and then enumerated. Randomly selected isolates from each location were screened for resistance to nine classes of antibiotics by disk diffusion, and the multiple antibiotic resistance (MAR) index was calculated. Numbers of total coliforms were significantly higher following rain compared to dry weather. Total coliform numbers were not significantly elevated at non-restricted wave action sites. Restricted wave action sites had a 78.5% increase in MAR index following wet weather compared to dry weather. Resistance to ampicillin was observed in almost 50% of isolates and was not significantly impacted by wave action or weather. Minimum inhibitory concentration testing revealed that many isolates were highly resistant to ampicillin. This study is the first to report on the antibiotic resistance of coliforms found in Southern California beaches and highlights the prevalence of ampicillin resistance.

Because of their lifestyles, abundance, and feeding habits, infaunal marine deposit feeders have a significant impact on the ocean floor. As these animals also ingest microorganisms associated with their sediment and seawater diet, their digestive tract usually contains a diverse array of bacteria. However, while most of these microorganisms are transients, some may become part of a resident gut microbiome, in particular when sheltered from the main flow of digesta in specialized gut compartments. Here, we provide an in-depth analysis of the structure and contents of the intestinal caecum (IC), a hindgut diverticulum found exclusively in schizasterid heart urchins (Echinoidea: Spatangoida: Schizasteridae). Based on specimens of Brisaster townsendi, in addition to various other schizasterid taxa, our structural characterization of the IC shows that the organ is a highly specialized gut compartment with unique structural properties. Next generation sequencing shows that the IC contains a microbial population composed predominantly of Bacteroidales, Desulfobacterales, and Spirochaetales. The microbiome of this gut compartment is significantly different in composition and lower in diversity than the microbial population in the sediment-filled main digestive tract. Inferences on the function and evolution of the IC and its microbiome suggest that this symbiosis plays a distinct role in host nutrition and that it evolved at least 66 million years ago during the final phase of the Mesozoic.

The California State University, Long Beach (CSULB) BUILDing Infrastructure Leading to Diversity (BUILD) program developed a near-peer mentoring component in which master's students serve as mentors for undergraduate research trainees in health-related disciplines, in addition to fulfilling teaching assistant duties. This paper has two parts. The first describes (a) the functions of this mentoring component, taking into consideration the context of CSULB; (b) the extensive year-round training curriculum for near-peer mentors; and (c) the evolution of this curriculum in response to feedback from BUILD trainees, near-peer mentors, and undergraduate research training instructors. The second part evaluates the effectiveness of the near-peer mentoring component, based on focus groups and quantitative surveys of both near-peer mentors and mentees. We offer recommendations for master's comprehensive research institutions interested in implementing near-peer mentoring within similar research training programs.

Phages greatly influence the ecology and evolution of their bacterial hosts; however, compared to hosts, a relatively low number of phages, especially halophilic phages, have been studied. This study describes a comparative investigation of physicochemical tolerance between a strain of the halophilic bacterium, Salicola, isolated from the Cargill Saltworks (Newark, CA, USA) and its associated phage. The host grew in media between pH 6–8.5, had a salinity growth optimum of 20% total salts (ranging from 10%–30%) and an upper temperature growth limit of 48 °C. The host utilized 61 of 190 substrates tested using BIOLOG Phenotype MicroArrays. The CGφ29 phage, one of only four reported Salicola phages, is a DNA virus of the Siphoviridae family. Overall, the phage tolerated a broader range of environmental conditions than its host (salinity 0–30% total salts; pH 3–9; upper thermal limit 80 °C) and is the most thermotolerant halophilic phage ever reported. This study is the most comprehensive investigation to date of a Salicola host–phage pair and provides novel insights into extreme environmental tolerances among bacteriophages.

Carnobacterium maltaromaticum is a well-known pathogen of bony fish. More recently, C. maltaromaticum have been isolated from the brain and inner ear of disorientated and stranded common thresher ( Alopias vulpinus ) and salmon shark ( Lamna ditropis ). While thresher shark strandings are recent, salmon sharks have been stranding for decades, suggesting a long-term association between C. maltaromaticum and sharks. Interestingly, some strains of C. maltaromaticum are used by the food industry for their probiotic and antimicrobial activity. Here, we sequenced the genome of 9 C. maltaromaticum strains (SK-isolates) from diseased common thresher and salmon sharks and compared them to other C. maltaromaticum strains in order to identify the genomic signatures that differentiate the disease-associated from the innocuous C. maltaromaticum isolates. SK strains formed a monophyletic clade, with a conserved gene repertoire, and shared a high degree of pseudogenization even though isolates were from different shark species, locations, and across years. In addition, these strains displayed few virulence associated genes and unique genomic regions, some resulting from horizontal gene transfer. The association of diseased sharks and SK strains suggests their role as potential pathogens. Although the high degree of pseudogenization suggests a transition to a host-adapted lifestyle, a set of conserved functional genes highlights the need of essential functions required for a host-independent life style. Globally, this work identifies specific genomic signatures of C. maltaromaticum strains isolated from infected sharks, provides the framework to elucidate the role of SK strains in the development of the disease in sharks, and further investigate the dissemination of SK strains in populations of wild fish.

The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities.

Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with (13)C-acetate, (15)N-ammonium, and (33)S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope ((13)C/(12)C, (15)N/(14)N, and (33)S/(32)S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

Carbon cycling by microbes has been recognized as the main mechanism of organic matter decomposition and export in coastal wetlands, yet very little is known about the functional diversity of specific groups of decomposers (e.g., bacteria) in salt marsh benthic trophic structure. Indeed, salt marsh sediment bacteria remain largely in a black box in terms of their diversity and functional roles within salt marsh benthic food web pathways. We used DNA stable isotope probing (SIP) utilizing 13C-labeled lignocellulose as a proxy to evaluate the fate of macrophyte-derived carbon in benthic salt marsh bacterial communities. Overall, 146 bacterial species were detected using SIP, of which only 12 lineages were shared between enriched and non-enriched communities. Abundant groups from the 13C-labeled community included Desulfosarcina, Spirochaeta, and Kangiella. This study is the first to use heavy-labeled lignocellulose to identify bacteria responsible for macrophyte carbon utilization in salt marsh sediments and will allow future studies to target specific lineages to elucidate their role in salt marsh carbon cycling and ultimately aid our understanding of the potential of salt marshes to store carbon.

Sulfate-reducing bacteria (SRB) are key mediators of anaerobic carbon cycling in coastal salt marsh sediments and have been shown to be important decomposer communities even in hypersaline habitats. Understanding how SRB function in various salt marsh habitats (vegetated, salt pans) is crucial to advancing our knowledge of salt marsh function. We compare overall sulfate reducing activity and the diversity of a subset of SRB (Desulfobacteriaceae) in two hypersaline sediments (salt pan and nearby area with desiccated vegetation) with a regularly inundated control site within the Huntington Beach Wetlands (HBW). Biological activity was quantified using radiotracer studies to measure sulfate reduction rates (SRR) with and without carbon amendment. All sites showed enhanced SRR under carbon amendment, suggesting short-term carbon limitation. Unique communities of Desulfobacteriaceae were found in all three sites with increased incidence of halotolerant genotypes in the salt pan. These findings indicate that, despite reduced anaerobic respiratory activity, highly diverse and functional deltaproteobacterial communities exist in salt pan and surrounding hypersaline habitats in coastal salt marshes in southern California.

The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA) evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 and 380 g l(-1) total salts, respectively) compared to Pond 9 (180 g l(-1) total salts). Both Pond 11 and 12 communities had high representation (47 and 45% of clones, respectively) by Haloquadratum walsbyi-like (99% similarity) lineages. The archaeal community in Pond 9 was dominated (79%) by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community). This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community) was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted.

Author(s): Dillon, Jesse; Whitcraft, Christine | Abstract: We hypothesized there would be differences in the microbial and infaunal communitiesprimarily responsible for degrading macrophyte vs. microalgal carbon. Specifically we predicted that: The invertebrate community degrading macrophyte-derived carbon will be significantly different from those degrading algal-derived carbon. The microbial communities (bacteria and fungi) degrading macrophyte-derived carbon will be significantly different from those not using this carbon source.