Biology subjects

Lampe, R. H.

Publications and source records attributed to Lampe, R. H..

5 recordsLinked to original sources

bioRxiv2025

Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem

Understanding the density of marine mammals is important for assessing population dynamics and evaluating the impacts of human activities on these species. In this work, we examine microorganisms that may be ecologically associated, whether directly or indirectly, with baleen whales - the potential "ecological habitat" - to predict baleen whale densities via statistical relationships adjusted for seasonal patterns of occurrence. We assessed the capability of microbial and small plankton communities to predict the density of Balaenopteridae whales in the Southern California Current Ecosystem in each quarterly season from 2014 to 2020 using data from the California Cooperative Oceanic Fisheries Investigations (CalCOFI). Densities were estimated from visual sightings for three target species - blue, fin, and humpback whales - and microbial and small plankton communities were examined using concurrent water samples via metabarcoding of the 16S and 18S rRNA genes. We identified microbial and small plankton communities specific to each target species that were strong predictors of estimated density. Groups of 23-60 distinct Amplicon Sequence Variants (ASVs) per baleen whale species explained 81-99% of variability in estimated whale density and predicted density estimates to within [~]1 individual per 1000 km2. The predictive accuracy achieved by our approach, compared with naive seasonal carry-forward and seasonal averaging approaches to prediction, improves out-of-sample RMSE by up to an estimated 65%. Microbial and small plankton communities were characterized by 148 unique taxonomic annotations enumerated across marker genes. Of these, 20% were shared across all three species, 21% were shared by two species, and the remaining (59%) were unique to a single whale species, which suggests that there is some overlap in the ecological habitat among blue, humpback, and fin whales, but each species is also related to a distinct community of microbes and small plankton. We also conducted a narrative review to examine existing known relationships of baleen whales with microbes or small plankton. Of the 148 unique taxonomic annotations we found to be predictive of baleen whale densities, 23% have been referenced within the existing literature exploring microbial prey, parasites, commensals, or respiratory-associated organisms of baleen whales, with matches at the genus or family level. The rest matched at higher taxonomic levels (41%) or had no documented matches in our literature search (36%). These findings suggest that some of the microbial and small plankton community predictors may be ecologically relevant, yet further studies are needed to understand how these organisms function collectively as a community and interact with whale ecology, prey, and the surrounding environment. Our results suggest that using microbial and small plankton communities to quantify the potential ecological habitat of larger organisms, like baleen whales, can enhance predictive models and may inform hypotheses about the ecological relationships between whales and the biological communities with which they co-occur.

ecology↗

bioRxiv2025

Atypical phosphatases drive dissolved organic phosphorus utilization by phosphorus-stressed phytoplankton in the California Current Ecosystem

In the ocean, dissolved organic phosphorus (DOP) supports the health and productivity of marine phytoplankton, a phenomenon most often investigated under inorganic phosphate (Pi) scarcity. However, microbial DOP acquisition occurring in Pi replete ocean environments remains poorly understood. Here, we conducted a combination of nutrient addition experiments, alkaline phosphatase (AP) rate measurements, and metatranscriptomics analyses along an onshore-to-offshore gradient in the California Current Ecosystem (CCE), a relatively Pi-rich upwelling region. We found that AP activity (APA) and eukaryotic transcripts for DOP utilization were present throughout the CCE. In bottle incubations, APA was upregulated in response to iron (Fe) and nitrogen (N) additions. Major contributors to these trends included atypical alkaline phosphatases (APaty) of diatoms in the coastal upwelling area, and unclassified non-cytoplasmic P-diesterases (PDEnc) of multiple eukaryotic taxa in the offshore regime. APA and gene expression dynamics were not coupled to phytoplankton growth, suggesting that these organisms experience underlying P stress, a state of cellular metabolism caused by Pi scarcity, even in regions primarily growth-limited by other elements. While APaty and PDEnc were highly abundant among the microbial community phosphatase pool, these genes were missing from a widely used annotation database, highlighting the importance of manual curation for the detection of these atypical and unclassified proteins. Altogether, these results emphasize the functional diversity of phosphatases sustaining microbial community health in diverse and productive marine habitats.

microbiology↗

bioRxiv2024

Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection

In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with this microbial milieux. Here, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple skin microbiome. We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Further, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin-and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly in the animals gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. ImportanceThe genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, non-pathogenic skin microbes or their function. We show that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animals cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.

microbiology↗

bioRxiv2020

Representative diatom and coccolithophore species exhibit divergent responses throughout simulated upwelling cycles

Wind-driven upwelling followed by relaxation results in cycles of cold nutrient-rich water fueling intense phytoplankton blooms followed by nutrient-depletion, bloom decline, and sinking of cells. Surviving cells at depth can then be vertically transported back to the surface with upwelled waters to seed another bloom. As a result of these cycles, phytoplankton communities in upwelling regions are transported through a wide range of light and nutrient conditions. Diatoms appear to be well-suited for these cycles, but their responses to them remain understudied. To investigate the bases for diatoms ecological success in upwelling environments, we employed laboratory simulations of a complete upwelling cycle with a common diatom, Chaetoceros decipiens, and coccolithophore, Emiliania huxleyi. We show that while both organisms exhibited physiological and transcriptomic plasticity, the diatom displayed a distinct response enabling it to rapidly shift-up growth rates and nitrate assimilation when returned to light and available nutrients following dark, nutrient-deplete conditions. As observed in natural diatom communities, C. decipiens highly expresses before upwelling, or frontloads, key transcriptional and nitrate assimilation genes coordinating its rapid response to upwelling conditions. Low iron simulations showed that C. decipiens is capable of maintaining this response when iron is limiting to growth, whereas E. huxleyi is not. Differential expression between iron treatments further revealed specific genes used by each organism under low iron availability. Overall, these results highlight the responses of two dominant phytoplankton groups to upwelling cycles, providing insight into the mechanisms fueling diatom blooms during upwelling events.

ecology↗

bioRxiv2018

Divergent gene expression among phytoplankton taxa in response to upwelling

Frequent blooms of phytoplankton occur in coastal upwelling zones creating hotspots of biological productivity in the ocean. As cold, nutrient-rich water is brought up to sunlit layers from depth, phytoplankton are also transported upwards to seed surface blooms that are often dominated by diatoms. The physiological response of phytoplankton to this process, commonly referred to as shift-up, is characterized by rapid growth rates and increases in nitrate assimilation. To examine the molecular underpinnings behind this phenomenon, metatranscriptomics was applied to a simulated upwelling experiment using natural phytoplankton communities from the California Upwelling Zone. An increase in diatom growth following five days of incubation was attributed to the genera Chaetoceros and Pseudo-nitzschia. Here we show that certain bloom-forming diatoms exhibit a distinct transcriptional response that coordinates shift-up where diatoms exhibited the greatest transcriptional change following upwelling; however, comparison of coexpressed genes exposed overrepresentation of distinct sets within each of the dominant phytoplankton groups. The analysis revealed that diatoms frontload genes involved in nitrogen assimilation likely in order to outcompete other groups for available nitrogen during upwelling events. We speculate that the evolutionary success of diatoms may be due, in part, to this proactive response to frequently encountered changes in their environment.

microbiology↗