Forest Response to Chronic Hurricane Disturbance in Coastal New England

Question: Hurricanes and cyclones cause a wide range of damage to coastal forests worldwide. Most of these storms are not catastrophic in ecological terms, but forest responses to storms of moderate intensities are poorly understood. In regions with a high frequency of moderate hurricanes, how does variation in disturbance intensity affect the magnitude of ecological responses? Location: Naushon Island, Massachusetts USA Methods: We use historical records and dendroecological methods to characterize establishment and growth of Fagus grandifolia, Quercus alba and Quercus velutina in response to seven non-catastrophic hurricanes of varying intensity and a major logging event, relative to baseline conditions, over the past ~ 150 years. Our aim was to document variation in the magnitude of responses to known disturbance events of varying intensity, and to determine whether tree growth after moderate hurricanes differs from growth during periods of no disturbance. Results: Forest harvesting in 1824-1827 had a strong impact on forest composition and growth. Since then, the study region has been characterized by little harvesting but frequent hurricanes. However, only one of the seven storms examined caused substantial increases in growth and new establishment for the dominant species; most moderate disturbances had minimal impacts on growth and regeneration dynamics. We also document highly variable responses among species to individual storms, including substantial growth decreases that may not be detected by standard analytical approaches. Conclusions: Our results caution against the use of simple metrics such as wind speed to predict forest response to specific hurricanes, and highlight the importance of individual disturbance events in controlling long-term forest dynamics, even in regions characterized by high disturbance frequency. Additionally, we show that standard approaches to reconstructing disturbance history based on increases in radial growth and pulses of tree establishment are likely to underestimate the frequency of moderate disturbances.Other Research Uni

A Hypothetical Bottleneck in the Plant Microbiome

The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe. Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe, we completed a more extensive survey of an additional 98 plant species representing 39 families. We again found that individual, surface-sterilized seeds of all species hosted only one PDA-culturable bacterial or fungal endophyte per seed, or none. PDA-unculturables were not determined but we expect them to also be bottlenecked in individual seeds, as they too should be governed by exclusionary interactions. If the bottleneck were confirmed with high-throughput sequencing of individual seeds then it would make sense to further investigate the Primary Symbiont Hypothesis (PSH). This includes the prediction that primary symbionts (i.e., the winners of the exclusionary battles among seed endophytes) have strong effects on seedlings depending on symbiont identity

Editorial: The role of dispersal and transmission in structuring microbial communities

Microbial communities influence the systems they inhabit by driving ecosystem processes and promoting the health and fitness of plant and animals hosts. While an extensive body of work has documented variation in microbial community membership across hosts and systems, understanding the drivers of this variation remains a challenge. Much of the focus of these efforts has been on the characterization of host variation or the abiotic environment, and has overlooked the role of dispersal, i.e., the movement of organisms across space, and transmission, i.e., the movement of microbes among environments, hosts and between hosts and their environment

Tare Soil Alters the Composition of the Developing Potato Rhizosphere Microbiome

Understanding the factors influencing microbial community composition in the rhizosphere is an important step toward managing the microbiomes of globally important crops such as potato (Solanum tuberosum). Potato is vegetatively propagated and seed tubers are planted with tare soil, or soil adhering to the tuber surface, from their field of origin. Bulk soil is known to influence rhizosphere microbiome composition but whether tare soil additionally contributes to compositional variation is not known. We tested this hypothesis in a greenhouse experiment where tare soil was removed (or remained intact for controls) prior to planting in either soil from a potato field or soil from a previously uncultivated area next the potato field. We used internal transcribed spacer and 16S metabarcoding to characterize the fungal and bacterial rhizosphere communities of plants grown from the experimental seed tubers. We found that tare soil influenced rhizosphere microbial composition, more strongly for fungi than bacteria. As expected, bulk soil origin explained the greatest amount of variation in the rhizosphere microbiome overall but we found no evidence that the impact of tare soil on microbial community composition differed between bulk soil origins. However, the magnitude of the tare soil effect did depend, in part, on seed tuber origin. Our findings reveal that tare soil explains a significant, though modest, amount of variation in rhizosphere composition, and sets the stage for future work addressing functional consequences for plant health and productivity

Protocols for investigating the leaf mycobiome using high-throughput DNA sequencing

High-throughput sequencing of taxon-specific loci, or DNA metabarcoding, has become an invaluable tool for investigating the composition of plant-associated fungal communities and for elucidating plant–fungal interactions. While sequencing fungal communities has become routine, there remain numerous potential sources of systematic error that can introduce biases and compromise metabarcoding data. This chapter presents a protocol for DNA metabarcoding of the leaf mycobiome based on current best practices to minimize errors through careful laboratory practices and validation

Characterizing Variation in the Bacterial and Fungal Tare Soil Microbiome of Seed Potato

For tuberizing crops such as potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used internal transcribed spacer and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potato plantlets used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potato plantlets that were collected from farmers in the Columbia Basin of Oregon. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and whether those communities influence plant health are essential steps towards potato microbiome management

Research priorities for harnessing plant microbiomes in sustainable agriculture.

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply

Research priorities for harnessing plant microbiomes in sustainable agriculture.

Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply