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Organismal interactions at the plant-fungal-soil interface

Plant species influence on rhizosphere microbes

Plant roots and root exudates are known to stimulate and change soil microbial communities and much research has been devoted to understanding these interactions in the rhizosphere. Questions such as do different plant species select for their own specific microbiome, and how these changes occur over time remained to be answered in context of agroecosystems. We are using different crop species important to Hawai`i to examine how plants can manipulate and change soil microbial and nematode communities over time. We will determine whether repeated planting of the same plant species can change the complexity in microbial diversity, interconnected and stability in microbial networks, and soil ecosystem services. We are also exploring specific mechanisms, such as how plant root exudates can select for beneficial microbes. Results from these studies will provide a biological dimension to soil health and allow us to sustainably leverage microbial resources for agriculture.

Microbial interactions in the hyphosphere

The ubiquity of fungal-bacterial interactions is only beginning to be understood. Fungi and bacteria are the most diverse and abundant microorganisms in the soil and we think that the results of their interactions can translate to major consequences in terrestrial ecosystems. We are exploring the diversity of fungal microbiomes and their interactions with their fungi hosts in various experiments, starting at the hyphal interface (aka the "fungal highway") where bacteria moves across environments, and scaling to the overall interactions between these organisms across our diverse soil systems. Here are some bacteria zipping along a Favolaschia calocera fungal highway in real time.

Soil biodiversity influences Soil Health

Measuring total soil biodiversity is one of the most basic, yet fundamental concepts that can contribute towards an integrative measure of soil health. It is generally understood that soil biodiversity matters for proper functioning of a healthy soil, but the basic understanding of the mechanisms of how soil biodiversity can drive a healthy soil is not well-understood. As a first step to developing a mechanistic understanding of the biological drivers of soil health, we will develop and streamline molecular tools that will enable rapid identification of soil biodiversity and integrate it into a more objective way of measuring soil health.

Fundamentals of fungal-plant mutualisms

Suillus, a model for ecology & coevolution of plant-fungal mutualisms

This transdisciplinary project combines modern systematics, ecology, and evolution to understand the mechanisms of host specificity, host generality, and host switching in plant-fungal mutualisms. The work is grounded in genome-enabled 'omics techniques through the sequencing of >50 Suillus species across the genus, as well as over 300 strains of the type species, Suillus luteus across the world. This effort generates a pangenome that enables our understanding of genomic bottlenecks and expansions from known time since isolation. Transcriptome data from mycorrhizal root-tips will help us understand the signals of host specificity and the mechanisms that allow certain strains to protect their hosts from heavy metals. This project establishes a powerful and flexible experimental system to study plant-fungal mutualism. More information about this project and collaborators can be found on the Suillus Consortium website. If you are interested in working on Suillus, send Nhu and email and we can write a post-doc or full research grant together.

Venturing aboveground and beyond

Warming effects on tropical soils

As our global temperature climbs dangerously higher, the impetus to understand the flow of soil carbon and other nutrients through soil biological system becomes increasingly important. There are currently multiple projects designed simulate soil warming, but most are located in temperate regions of the world. Our lab works in collaboration with Dr. Susan Crow to understand microbial and nutrient changes in volcanic Andisols. We will explore how microbes contribute sequestering and removal of protected carbon from these soils.

Microbes, health and flavor in Hawaiʻi grown cacao

The proper fermentation of cacao beans is an an essential part in producing great chocolate. Most cacao fermentation use microorganisms that live on plant/pod surfaces, and we think that these microbes can contribute to the overall development of flavors in the final product. We are identifying the microbes on the surface of cacao pods across multiple varieties and locations on Oʻahu to determine whether microorganisms play an important role in the terroir of the chocolates. Belowground, we are testing microbial inoculants, especially mycorrhizae, to determine whether they can provide benefits to establishing plants, and whether these inoculants continue to provide benefits to pod-producing plants. These projects are in collaboration with Drs. H. C. Skip Bittenbinder, Daniela Elliot (Leeward Community College), and Dave Elliot (O'ahu RCD).

On-going synthesis projects


We continuously update our FUNGuild system to assign ecological guilds to fungal taxa. Nhu continues collaboration with Peter Kennedy, Scott Bates, Zewei Song to maintain and improve the FUNGuild database, adding more entries and improving performance. This system is quickly becoming useful to a wide range of researchers in fungal ecology. Further, Scott & Nhu are working to extend the use of the parsing system to other biological groups including nematodes and arthropods. If you would like to contribute your guild data to improve our databases, please email Nhu.

Macro and micro Fungi of Hawaiʻi

Fungi are one of the most diverse groups of organisms on the planet. Macrofungi (those with conspicuous fruiting bodies such as mushrooms) are generally well recorded, but the microfungi (those that are small or microscopic) are much less documented. The goal of this project is to contribute to the growing list of macrofungi in Hawaiʻi, starting from the book "Mushrooms of Hawaiʻi" by Hemmes & Dejardin", as well as DNA documentation of the microfungi. Sequence data from our projects in the lab, as well as from other fungal labs in Hawaiʻi contributes to the overall goal of this project.

Soil microbiome of the Hawaiian Islands

The soil is arguably the most complex environment in which to study microbes, and it is this same complexity that leads to the overwhelming diversity of soil microorganisms (speaking broadly including prokaryotes, fungi, and protists). The aim of this project is to catalogue the identity, richness, and genetic diversity of microbial organisms in both agricultural and natural ecosystems across the Hawaiian Islands. The culmination of many current and past lab projects contribute the underlying data for the concept of the Soil Microbiome of the Hawaiian Islands.

Past projects

Nodulating rhizobia in native and non-native legumes

We know that legume-nodulating rhizobia are common in our soils, but which species of rhizobia associates with native and non-native plants? Can we isolate and use them in native plant restoration efforts? Jon Abe, an undergraduate in the lab created and drove this project to isolate, identify, and produce inoculum resources that are available to restoration and agricultural efforts in the state. The UH Mānoa's Undergraduate Research Opportunity Program (UROP) provided Jon with a grant to do this work!

Results from this project: Rhizobia of Hawaiʻi

Microbiome of Waimea Valley

No living organism exists in isolation. Each exists and interact with a consortium of microbial organisms known as the microbiome. We explore our physical landscapes and study the microbiomes of various larger organisms (plant, fungi, animals) and substrates (soil, water, air) through various projects and collaborations. A current major project towards this effort is the Microbiome of the Waimea Ahupuaʻa (watershed), an ambitious project led by a consortium of UH faculty in the Center for Microbiome Analysis and Island Knowledge (C-MAIKI).