Some of the most recent projects in the lab are focused on testing the theory of community assembly and address the role of both deterministic (e.g., biogeochemical soil properties, diversity of plants and soil microbes, and traits of species) as well as stochastic (e.g., species pool size and history of species arrival) factors. To test these factors, we conduct observational and experimental studies across environmental gradients in high alpine and polar ecosystems.
Here is a list of some of our current ongoing projects:
EFFECTS OF CLIMATE WARMING ON SOIL COMMUNITIES IN THE COLORADO ROCKY MOUNTAINS.
The history of life, evolution, and diversity have all been associated with environmental change of some natural factors. However, over the last century, the natural world has been grappling with human-induced change that can place life and entire ecosystems on very different trajectories. Among human-induced environmental change factors, climate change, and specifically, climate warming, is one of the most notable.
Species can respond to climate warming in various ways, but one of the most common strategies involves a move to higher latitudes and altitudes resulting in global redistribution of species. This response has been fairly well documented in terrestrial ecosystems for aboveground macroscopic species (e.g., plants and insects), but for belowground microscopic species, including nematodes, is largely unknown.
One ecosystem that experiences very clear effects of climate warming is the high alpine region in the Colorado Rocky Mountains. The site of our study, the Niwot Ridge, spans the higher edge of alpine tundra and expands above 3600 m.a.s.l. Over the last 50 years, climate warming has increased average temperatures and reduced snow cover. In turn, these changes in temperature and snow cover have resulted in progressive migration of plants into the talus bare soils creating a gradient of terrestrial environments ranging from bare ground to increasingly vegetated. We use this natural plant succession gradient to study potential shifts in the distribution patterns of microbial communities and how they affect soil processes. In other words, we want to know whether soil biota track climate in similar ways that plants do.
EXTREME ENVIRONMENTS - ALKALINE LAKES
The Alkaline Lakes region in the Sandhills of Nebraska provide an unusual natural experiment with a gradient of solute concentrations and alkalinity. We study microbial communities and measure biogeochemical characteristics along this extreme chemical gradient to examine how patterns of biodiversity develop, how organisms adapt, and what processes drive them. In addition, we investigate how changes associated with climate warming may affect these patterns.
PRIMARY SUCCESSION AND COMMUNITY ASSEMBLY
As humans exert more influence on climate warming, glaciers recede at faster and faster rates. As glaciers recede, the distance from the glacier to the newly exposed terrain can be used as a clock to document the process of ecological succession. Theoretically, soils closest to glaciers’ termini are the youngest and as the distance increases, so does the age of soils. Therefore, the space of a chronosequence can be substituted for time.
Primary succession and community assembly are fundamental ecological process in these early developing soils but have mainly focused on changes of aboveground plant communities. How the different components of soil communities assemble within forefields of receding glaciers is still largely unknown. Deglaciated forefields of the high elevation (~5000 m.a.s.l.) Puca Glacier in the Peruvian Andes provides a site for one of our studies on primary succession. To examine the process of succession of the entire soil community, we established sampling plots at three different locations representing 9-, 24-, and 89-year old deglaciated soils. Our main objectives are to examine: 1) the diversity and composition of the entire soil community (bacteria, fungi, non-fungal eukaryotes, and nematodes) along the Puca Glacier’s chronosequence, 2) potential functional roles of groups of organisms in the soil community succession, and 3) relationships between soil community composition and edaphic factors and microbial activity.
Another model system for testing how communities assemble is also associated with glaciers, but this time we study communities that develop on the surface of glaciers, and more specifically, in cryoconite holes. Cryoconite holes form on glaciers when soils and sediments blown by wind settle on glaciers’ surface. As they absorb more solar radiation than the surrounding ice, they melt into the ice and eventually form bucket-sized holes with the sediment layer at the bottom. Each hole becomes its own independent ecosystem with its own trophic foodweb. Cyanobacteria and algae are the primary producers, fungi and heterotrophic bacteria as the decomposers, and microinvertebrates (i.e., tardigrades and rotifers) as the grazers.
Because cryoconite holes are largely independent from each other and last from a few years to a decade, we can track the development of microbial communities within these holes and examine the role of stochastic and deterministic factors that might shape these communities. A major component of our work involves doing surveys of cryoconite holes located on different glaciers in the Taylor Valley, Antarctica. In addition to studying natural holes, we can also create experimental holes to target specific questions (e.g., does the initial diversity/complexity of the seeding sediment play a role in how communities develop).
NEMATODE GUT MICROBIOME
The phylum Nematoda is considered one of the most abundant and diverse animal taxa. In addition to their taxonomic diversity, they display a wide array of feeding habits that are classified by morphology of their mouth parts. For example, bacterial feeders have narrow tube-like stoma vs. plant feeders which have hypodermic needle-like stylets. Through their feeding habits, nematodes play important roles in soil foodwebs. For example, by feeding on bacteria and fungi they contribute of C- and N-mineralization and by preying on other organisms like rotifers and tardigrades, they contribute to regulation of their populations.
Despite this general knowledge of feeding habits, the knowledge of the actual food sources is restricted to wide categories like bacteria or fungi. However, emerging evidence from gut microbiome studies indicates that microbiome assemblages are highly specific and that they are crucial to their host's biology.
In the Antarctic Dry Valleys, nematode communities are incredibly simple as they consist of mainly three species, two of which are bacterial feeders (Scottnema lindsayae and Plectus murrayi) and the third is an omnivore (Eudorylaimus antarcticus). Because each species is morphologically distinct, we can study the nematode-gut microbiome relationships at the species level, something that would be difficult in any other environment which would likely host multiple species that are morphologically indistinguishable.
In this project, we examine gut microbiomes of nematodes living in different types of algal mats (black and orange). The mats grow for ~10 weeks in streams that are fed by melting glaciers during austral summers. In addition to nematodes, the mats host other organisms including diverse bacteria, fungi, protists, and rotifers and tardigrades. Since the same nematode species occupy different mat in different streams across a large scale (the Taylor Valley) diversity gradient, they lend themselves as a perfect model system for answering questions about specificity of feeding habits.
MANAGEMENT OF PLANT PARASITIC NEMATODES
Root-knot nematodes are an important soilborne pathogen of all crops grown in Florida. In total, 14 Meloidogyne species have been identified including M. incognita, M. arenaria, M. javanica, M. floridensis, M. enterolobii, and M. haplanaria all of which have broad host ranges. Another species slowly gaining momentum is Meloidogyne partityla that infects pecan trees and reduces tree vigor, yields, and longevity. Although M. partityla is reported as the most important species infecting pecans, the significance of the other root-knot nematodes present in Florida to pecan industry has not been evaluated.In addition, M. partityla has been recently recovered from several native species of oak but no information is available on whether the species found on oak infects pecans or vice versa. As the pecan industry is undergoing resurgence in Florida due to its high nut value and increased interest of export to China, detailed information on which root-knot nematodes infect pecans on farms and in nurseries, what damage they can inflict, and how they can be best managed is much needed.
The overall goal of this project is to better understand the root-knot nematode disease on pecans, and to elucidate the role of different species of root-knot nematodes on pecans.
MITOMETAGENOMICS FOR IDENTIFICATION OF NEMATODE SPECIES
Understanding nematode diversity requires the knowledge of species identity. Nematode species identification based on morphology, the currently predominant tool, is slow and frankly unreliable. Although molecular tools based on Sanger and amplicon high-throughput sequencing (HTS) of rDNA gene markers (e.g., 18S, 28S, and ITS) have provided for an improved ability of nematode identification, they are often inappropriate for species-level resolution. Among the more promising markers are those derived from the mitochondrial genome, and in particular the mitochondrial cytochrome oxidase c subunit 1 (COI) gene, the barcode for animals. Unfortunately, the hypervariable nature of the priming region of the COI gene in Nematoda allows only for low-throughput sequencing (a few species from a few individuals at a time) that prohibits large biodiversity studies. In addition, a single COI gene has insufficient variation to separate some important nematode species (e.g., the mitotic parthenogenetic tropical root-knot subgroup). A potential solution to this problem is HTS shot-gun sequencing of the entire mitochondrial genomes. The main objective of this project to improve diagnostic capacity for nematode species identification by developing and testing a mitochondrial metagenomic protocol (Nema-mtMG).
Because taxonomic assignment to generated sequences can only be as good as a reference database that provides for annotation, the second objective of this project is develop a curated in-house mitochondrial database, Nema-mtDB. This database is getting organized via several ways: 1. collating sequencing information from officially existing resources (e.g., BOLD, QBOL, Miduri, and NR-NCBI reference databases) and private collections of taxonomist colleagues and collaborators into a COI reference database compatible with HTS data processing and analysis, 2. extending beyond the COI database to include full mitochondrial genomes emphasizing all protein coding genes by shot-gun sequencing of mitochondrial genomes from individual nematode species from cultures, 3. Same as above but from environmental samples.
The usability of the Nema-mtMG protocol requires bioninformatic tools that allow for data processing, analysis, and synthesis in concert with the mitochondrial database. The third objective of this project is the development of such tools, pipelines, and training materials.