Biology subjects

Amend, A. S.

Publications and source records attributed to Amend, A. S..

7 recordsLinked to original sources

bioRxiv2026

Coconut filters woven using Native Hawaiian techniques capture coastal microplastic and sunscreen pollution and support fungal bioremediation

Microplastic pollution and sunscreen contaminants increasingly threaten coastal ecosystems, yet many existing clean-up solutions rely on synthetic materials, creating additional carbon emissions during manufacturing, or address pollutant removal without subsequent treatment, leaving risk of future run-off back into the ocean. Here we evaluate coconut husk, an abundant and biodegradable agricultural byproduct, as a dual-function platform for physical pollutant capture and microbial bioremediation applications. To test the natural microbial community of coconuts for bioremediation potential, we isolated fungi from coconut husks and screened their growth under plastic- and sunscreen-containing conditions. 24 fungal isolates grew on plastic- and/or sunscreen media, with several isolates belonging to genera previously documented to degrade plastic, i.e. Chaetomium, Curvularia, Meyerozyma, Cladosporium, and Fusarium. We then developed filtration modules using coconut husks, fiber, and leaves, basing our design on traditional Hawaiian papale lau niu (coconut leaf hat) weaving. In filtration trials, the woven devices captured up to 76.58 +/- 3.73% of suspended microplastic particles in 2 minutes and captured suspended sunscreen with a 533.51 +/- 0.81 NTU decrease in net turbidity of the surrounding water than in control trials with no filter. Overall, this work introduces a form of natural innovation for pollution clean-up, building on coconut-based materials, traditional techniques, and microbial resilience to create a sustainable and cost-effective system.

microbiology↗

bioRxiv2025

Diversity, connectivity and negative interactions define robust microbiome networks across land, stream, and sea

In this era of rapid global change, factors influencing the stability of ecosystems and their functions have come into the spotlight. For decades the relationship between stability and complexity has been investigated in modeled and empirical systems, yet results remain largely context dependent. To overcome this we leverage a multiscale inventory of fungi and bacteria ranging from single sites along an environmental gradient, to habitats inclusive of land, sea and stream, to an entire watershed. We use networks to assess the relationship between microbiome complexity and robustness and identify fundamental principles of stability. We demonstrate that while some facets of complexity are positively associated with robustness, others are not. Beyond positive biodiversity x robustness relationships we find that the number of "gatekeeper" species or those that are highly connected and central within their networks, and the proportion of predicted negative interactions are universal indicators of robust microbiomes. With the potential promise of microbiome engineering to address global challenges ranging from human to ecosystem health we identify properties of microbiomes for future experimental studies that may enhance their stability. We emphasize that features beyond biodiversity and additional characteristics beyond stability such as adaptability should be considered in these efforts.

ecology↗

bioRxiv2021

specificity : an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria.

BackgroundUnderstanding the factors that influence microbes environmental distributions is important for deter-mining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Raos (1982, 2010) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables. ResultsWe present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well. Conclusionsspecificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificitys companion package, specificity.shiny.

microbiology↗

bioRxiv2020

Multiscale interactions between plant part and a steep environmental gradient determine plant microbial composition in a tropical watershed

Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. Interactions between these scales, however, are seldom considered. Here we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep environmental gradient within a single Hawaiian watershed. At each location we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. While the composition of microbial communities is driven primarily by microhabitat, this variable predicted more than twice the compositional variance for bacteria compared to fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacteria. Additionally, the spatial dynamics of fungal communities differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings identify potential differences underlying the mechanisms shaping communities of fungi and bacteria associated with plants, and indicate an interaction between assembly mechanisms working simultaneously on different spatial scales.

microbiology↗

bioRxiv2020

Scale-dependent influences of distance and vegetation on the composition of aboveground and belowground tropical fungal communities

Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific. Fungal communities exhibited strong distance decay of similarity across our entire sampling range (3-110,000 m), and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales, and tree community composition at large scales. We demonstrate scale-dependent spatial dynamics of fungal communities, synchronous spatial dynamics for trees and fungi, and the varying influence of habitat versus geographic distance in structuring Soil, Selaginella sp., and Understory fungal communities.

ecology↗

bioRxiv2019

Plant-microbe specificity varies as a function of elevation

Specialized associations between interacting species are a fundamental determinant of the diversity and distribution of both partners. How specialization of guilds of organisms varies along environmental gradients underpins popular theories of biogeography and macroecology, whereas the degree of specialization of a species is typically considered fixed. However, the extent to which environmental context impacts specialization dynamics is seldom examined empirically. In this study, we examine how specialization within a bipartite network consisting of three co-occurring plant species and their foliar fungal endophyte symbionts changes along a 1 000-meter elevation gradient where host species were held constant. The gradient, along the slope of Mauna Loa shield volcano, represents the entire elevational range of two of the three plants. Network and plant specialization values displayed a parabolic relationship with elevation, and were highest at middle elevations, whereas bipartite associations were least specific at low and high elevations. Shannons diversity of fungal endophytes negatively correlated with specificity, and was highest at the ends of the transects. Although plant host was a strong determinant of fungal community composition within sites, fungal species turnover was high among sites and plant host predicted a weak, though significant proportion of compositional variance. There was no evidence of spatial or elevational patterning in fungal community compositon. Our work demonstrates that specificity can be a plastic trait which is influenced by the environment and centrality of the host within its natural range.

ecology↗

bioRxiv2019

Foliar fungi alter reproductive timing and allocation in Arabidopsis under normal and water-stressed conditions

Microbes influence plant phenotypes but most known examples of this are from the study of below-ground microbes and plant disease modification. To examine the potential importance of phyllosphere microbes on non-disease related plant traits, we used sterile Arabidopsis clones to test the effects of foliar fungi on flowering phenology and reproductive allocation under conditions of varying water stress. We inoculated the sterile plants with fully-factorial combinations of four fungal isolates, then measured flowering time and reproductive allocation for each treatment group under normal and water-stressed conditions. All plants inoculated with foliar fungi had significantly later flowering and greater seed mass than the sterile control groups. The magnitude of this effect depended on the specific fungi present, but individual fungal effects diminished as inoculum richness increased. Above-ground microbes likely influence other plant traits as well and should be considered in any study measuring plant phenotypes.

plant biology↗