The unseen world: environmental microbial sequencing and identification methods for ecologists

Archaea, bacteria, microeukaryotes, and the viruses that infect them (collectively “microorganisms”) are foundational components of all ecosystems, inhabiting almost every imaginable environment and comprising the majority of the planet’s organismal and evolutionary diversity. Microorganisms play integral roles in ecosystem functioning; are important in the biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorus (P), and various metals (eg Barnard et al. 2005); and may be vital to ecosystem responses to large-scale climatic change (Mackelprang et al. 2011). Rarely found alone, microorganisms often form complex communities that are dynamic in space and time (Martiny et al. 2006). For these and other reasons, ecologists and environmental scientists have become increasingly interested in understanding microbial dynamics in ecosystems. Ecological studies of microbes in the environment generally focus on determining which organisms are present and what functional roles they are playing or could play. Rapid advances in molecular and bioinformatic approaches over the past decade have dramatically reduced the difficulty and cost of addressing such questions (Figure 1; WebTable 1). Yet the range of methodologies currently in use and the rapid pace of their ongoing development can be daunting for researchers unaccustomed to these technologies

Native and invasive inoculation sources modify fungal community assembly and biomass production of a chaparral shrub

Feedbacks between plants and surrounding soil microbes can contribute to the establishment and persistence of invasive annual grasses as well as limit the success of restoration efforts. In this study, we aim to understand how three sources of soil inocula – native, invasive (from under Bromus diandrus) and sterile – affect the growth response and fungal community composition in the roots of a chaparral shrub, Adenostoma fasciculatum. We grew A. fasciculatum from seed in a greenhouse with each inoculum source and harvested at six months. We measured above- and below-ground biomass, arbuscular mycorrhizal fungal (AMF) colonization and conducted targeted-amplicon sequencing of the 18S and ITS2 loci to characterize AMF and general fungal community composition, respectively. Native inoculum resulted in roots with richer communities of some groups of AMF and non-AMF symbionts, when compared to roots grown with invasive or sterile inoculum. Seedlings grown with invasive and native inoculum did not have different growth responses, but both produced more biomass than a sterile control. These findings suggest that inoculation with soil from native species can increase the diversity of multiple groups of fungal symbionts and inoculation with live soil (invasive or native) can increase seedling biomass. Moreover, future work would benefit from assessing if a more diverse community of fungal symbionts increases seedling survival when planted in field restoration sites

Impacts of Invasive Plants on Soil Fungi and Implications for Restoration

Biological plant invasions impact the function and biodiversity of ecosystems across the globe by displacing native plant species and altering the physical and chemical soil environment. While much is known about direct competition between invasive and native plants, ecologists have just begun to uncover the less obvious impact of plant invasion: changes to the soil fungal community. Fungi are important to the survival of many plant species and an integral part of a healthy soil system. Arbuscular mycorrhizal fungi are plant mutualistic symbionts that associate with many species and provide necessary services, such as increasing surface area for root water absorption and resistance to pathogens, while ectomycorrhizal fungi play an equally important role and are critical for plant nutrient acquisition in boreal and temperate forests. Invasive plants are altering the soil fungal community in ways that indirectly impact the structure of native plant communities, sometimes for years after the invasive plant has been removed from an area (i.e., legacy effects). These changes make restoration especially difficult in areas from which long-term plant invasions have been eradicated; in some cases these changes can be so severe that even with active management, they take months or decades to reverse

Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea

Shifts in microbial communities driven by anthropogenic nitrogen (N) addition have broad-scale ecological consequences. However, responses of microbial groups to exogenous N supply vary considerably across studies, hindering efforts to predict community changes. We used meta-analytical techniques to explore how amoA gene abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) respond to N addition, and found that N addition increased AOA and AOB abundances by an average of 27% and 326%, respectively. Responses of AOB varied by study type, ecosystem, fertilizer type, and soil pH, and were strongest in unmanaged wildland soils and soils fertilized with inorganic N sources. Increases in nitrification potential with N addition significantly correlated with only AOB. Our analyses suggest that elevated N supply enhances soil nitrification potential by increasing AOB populations, and that this effect may be most pronounced in unmanaged wildland soils

Leaf-cutter ants - mycorrhizal fungi: observations and research questions from an unexpected mutualism.

Leaf-cutter ants (LCAs) are widely distributed and alter the physical and biotic architecture above and below ground. In neotropical rainforests, they create aboveground and belowground disturbance gaps that facilitate oxygen and carbon dioxide exchange. Within the hyperdiverse neotropical rainforests, arbuscular mycorrhizal (AM) fungi occupy nearly all of the forest floor. Nearly every cubic centimeter of soil contains a network of hyphae of Glomeromycotina, fungi that form arbuscular mycorrhizae. Our broad question is as follows: how can alternative mycorrhizae, which are-especially ectomycorrhizae-essential for the survival of some plant species, become established? Specifically, is there an ant-mycorrhizal fungus interaction that facilitates their establishment in these hyperdiverse ecosystems? In one lowland Costa Rican rainforest, nests of the LCA Atta cephalotes cover approximately 1.2% of the land surface that is broadly scattered throughout the forest. On sequencing the DNA from soil organisms, we found the inocula of many AM fungi in their nests, but the nests also contained the inocula of ectomycorrhizal, orchid mycorrhizal, and ericoid mycorrhizal fungi, including Scleroderma sinnamariense, a fungus critical to Gnetum leyboldii, an obligate ectomycorrhizal plant. When the nests were abandoned, new root growth into the nest offered opportunities for new mycorrhizal associations to develop. Thus, the patches created by LCAs appear to be crucial sites for the establishment and survival of shifting mycorrhizal plant-fungal associations, in turn facilitating the high diversity of these communities. A better understanding of the interactions of organisms, including cross-kingdom and ant-mycorrhizal fungal interactions, would improve our understanding of how these ecosystems might tolerate environmental change