Nematodes, also known as roundworms, are among the most abundant groups of animals on the planet. If you had pinworms as a child, you’ve experienced nematodes firsthand – and are not alone, as at any given time, about a third of the world’s population is believed to be infected by some kind of nematode para- site. Nematodes, many species of which are not parasitic, are also incredibly common denizens of coastal sediments, and an important source of nourishment for shellfish and bigger worms, which themselves are forage species for other animals. Because of this, roundworms are critical components of the coastal food web, and hence a meaningful “bottom-up” indicator of coastal ecosystem functioning.

Vernal pools are ephemeral wetlands, typically with a diverse and highly adapted flora and fauna. We conducted the first nematode survey on record for this ecologically important habitat. Soil samples were collected on six dates from four locations in and around each of two vernal pool basins in the Santa Rosa Plateau Ecological Reserve. Nematodes from plant roots and debris were extracted in a mist chamber separately from the rest of the soil, which was sieved. An estimated fifty-two nematode genera were isolated, including at least sixty-three species. Soils from the two pools were substantially different in the composition and dynamics of their nematode communities. Nematode abundances were analyzed using the nonparametric Friedman test. Significant differences are observed between/among exact locations, sample dates and extracted sample fractions. Differences in abundance patterns are also significant across nematode genera. Simple feeding experiments were conducted to test whether some vernal pool nematodes might feed on the cysts of fairy shrimp, and thereby potentially limit the recovery of some endangered fairy shrimp species. Our observations do not suggest that this is the case. During the dry summer phase, roots and plant debris appear to play an important role in both pools as refuges for nematodes, and by extension of microscopic organisms in general. Adults of large nematodes, in genera such as Dorylaimus and Labronemella congregate preferentially in dead plant material, perhaps not only in response to drought but also because of the fine texture of the underlying soil. “Aquatic” genera such as Tobrilus persist throughout the dry phase, especially in plant debris. We recommend that management of vernal pools takes care to avoid controlled burns or other forms of removal of dead plant material in dry vernal pool beds. Future surveys of nematodes and other microscopic organisms in this type of alternately inundated and desiccated habitat should include methods for extraction of roots and plant debris.

The Bolsa Chica Wetlands have undergone extensive engineering works in 2004-2007 to restore different levels of tidal action in different sectors of the wetlands. Different properties of nematode communities can be used to make management decisions and evaluate restoration success. Published studies have shown among others that nematode abundance increases, while their diversity and evenness decrease, in conditions of nutrient enrichment. From past observations we hypothesize that the following spatial and temporal patterns will occur in Bolsa Chica:

- From the beginning of our sampling efforts, we expect to find that Outer Bolsa Bay harbors fewer nematodes, but more species and more equitable numbers per species, compared to Inner Bolsa Bay.

- As the effects of tidal restoration kick in, we expect to find progressively more species and evenness but lower abundance in the full tidal restoration area.

- As the effects of tidal restoration kick in, we expect to find a more moderate increase in species and evenness versus a moderate drop in abundance in the muted tidal restoration area.

- Additionally, we expect a significant change in the taxonomic composition of nematodes in the two restoration sectors.

The meiofauna is abundant and diverse, occupying key roles in sediment food webs and nutrient cycling, and responds rapidly to environmental changes. Nematodes and copepods usually constitute the major components of the meiofauna. As well as being a large part of the meiofauna, nematodes are the most abundant and most diverse invertebrates in many sediments and soils. They occupy a wide variety of ecological roles in sediments, and their community structure provides important clues to the structure of benthic foodwebs, as well as to responses of sediment ecosystems to environmental changes such as pollution and changes in tidal range. Despite the advantages of using nematodes for biomonitoring, they are used less frequently than other groups due to some major limitations, including the so-called "taxonomic impediment". Some aspects of this impediment are illustrated via the description of new free-living nematode species. One limitation is the scarcity of expert marine nematode taxonomists and the concentration of these experts mainly in Europe. The present study is the first to investigate Californian coastal nematodes to address environmental concerns in California, specifically the restoration-in-progress of the Bolsa Chica wetland. In common practice, nematode studies usually refrain from analyzing species-level differences between sites and communities, settling instead for genus or family level identifications by way of more feasible compromise. This choice is made perforce by the challenges of working with nematodes, and meiofauna in general. Part of the present study examined whether this choice is justified in the case of free-living marine nematodes. New molecular methods present opportunities to improve biomonitoring. Whole DNA extracts from a sediment core can be subjected to massively parallel pyrosequencing of taxonomically distinctive DNA loci, producing in one procedure a comprehensive list of the great majority of interstitial invertebrates living in that sediment across most animal phyla. Determining how the detailed and relatively robust phylogenies created with these new molecular tools can be incorporated in the study of biodiversity is an important research area, as biodiversity is the main facet of biomonitoring.

Microbial populations observed in the microbiome of Acrobeloides maximus consistently comprised a set of different microorganisms compared to the microbiome of Caenorhabditis elegans or the metagenome of the soil sample to which nematodes were exposed. Using 16S rRNA gene amplification, the bacterial genera Ochrobactrum, Pedobacter, and Chitinophaga were identified at significant levels within the A. maximus communities only and were found to be consistently present during each of the three sampling periods over six months. We were able to isolate and grow colonies of Ochrobactrum and Pedobacter from the microbiome of the nematode on Lysogeny Broth-Miller (LB) and Yeast Extract (YE) agar plates. We were unable to isolate the associate from the genus Chitinophaga. The results obtained suggest a possible specific and persistent association between A. maximus and the two bacterial isolates we were able to culture.

With fluorescence in situ hybridization (FISH) with probes specific for Ochrobactrum and Pedobacter, we were able to stain these bacterial cells and show that they reside within the intestinal tract of A. maximus. It is possible that these gut bacteria may be mutualistic by providing A. maximus with essential metabolites, by aiding the nematode in the digestion of other bacteria, or by providing it with protection against pathogens.

Using 16S rRNA amplification and sequencing, three bacterial strains belonging to the genera Ochrobactrum, Pedobacter, and Chitinophaga were detected at significant levels within cultured Acrobeloides maximus populations exposed to soil for 24 hours before extraction and re-inoculation on agar. All three strains were found to persist in re-inoculated A. maximus cultures over a period of six months. For each strain, sequences from our A. maximus associated clones along with relevant 16S rRNA sequences from congeners or related genera available in GenBank were subjected to comprehensive phylogenetic analyses. Sequences were aligned using the multiple sequence alignment algorithms implemented in T-Coffee, MAFFT, Kalign, and WebPRANK, and phylogenetic trees were constructed using Bayesian and maximum-likelihood methods. Similarities and differences among the different alignment and tree-building methods suggest tree building methods with T-Coffee performed more poorly while maximum-likelihood methods with MAFFT and Kalign produced more mutually consistent topologies that correspond better to recognized genus boundaries. Inferences are made about the known species that are phylogenetically closest to each of our three strains. Our Ochrobactrum strains appear to be most closely related to Ochrobactrum tritici, while our Chitinophaga strains are most similar to a bacterium previously identified as “Flexibacter cf. sancti.” Our Pedobacter strains seem to be a previously undescribed sphingobacterium within the genus.

Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at 4 sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyano-lichen, Green-algal lichen, Smooth-moss, and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics 1) central versus southern Mojave sites displayed different community signatures, 2) indicator taxa of plant associated fungi (plant pathogens and wood saprotrophs) were identified at each site, 3) surface and subsurface microbial communities were distinct, and 4) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples, with Actinobacteria, Proteobacteria, Cyanobacteria, and Ascomycota as hubs among all phyla. Specifically, the genera with highest node degree was Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) in bacteria and Alternaria sp. (Pleosporales, Ascomycota) among fungal genera. Our findings provide crucial insights for dryland microbial community ecology, conservation, and sustainable management.

Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at 4 sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyano-lichen, Green-algal lichen, Smooth-moss, and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics 1) central versus southern Mojave sites displayed different community signatures, 2) indicator taxa of plant associated fungi (plant pathogens and wood saprotrophs) were identified at each site, 3) surface and subsurface microbial communities were distinct, and 4) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples, with Actinobacteria, Proteobacteria, Cyanobacteria, and Ascomycota as hubs among all phyla. Specifically, the genera with highest node degree was Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) in bacteria and Alternaria sp. (Pleosporales, Ascomycota) among fungal genera. Our findings provide crucial insights for dryland microbial community ecology, conservation, and sustainable management.