Katherine E. French

Bio: Katherine E. French is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Bioremediation & Grassland. The author has an hindex of 7, co-authored 22 publications receiving 171 citations. Previous affiliations of Katherine E. French include University of Oxford.

Conversion of grassland to arable decreases microbial diversity and alters community composition

Abstract: The rapid global conversion of biodiverse landscapes to intensively managed arable fields may decrease microbial diversity and threaten the long-term fertility of native soils. Previous laboratory and experimental studies provide conflicting results: some have recorded declines in overall microbial diversity and certain beneficial microorganisms under intensified cultivation while others report no change (or even increased) diversity. However, few studies have been carried out in actual agricultural fields. We analysed the soil metagenomic communities of 36 current and former grasslands in Oxfordshire, England using Illumina sequencing of the bacterial 16S and fungal ITS1 regions to examine how agricultural intensification alters native microbial communities and whether arable reversion can reverse these processes. We demonstrate that land-use change did not affect bacterial diversity or specific beneficial taxa (nitrogen-fixing bacteria and mycorrhizas). However, fungal diversity declined and certain microbiota known to be plant pathogens (e.g. Olpidium) were significantly more abundant on agriculturally improved fields. On sites where arable reversion took place, microbial communities were similar to those from unimproved grasslands although overall vegetation diversity and fungal richness were lower. The conservation of species-rich grasslands and their associated microbial diversity could therefore be a key resource for sustainable agriculture in the future.

Engineering Mycorrhizal Symbioses to Alter Plant Metabolism and Improve Crop Health.

Abstract: Creating sustainable bioeconomies for the 21st century relies on optimizing the use of biological resources to improve agricultural productivity and create new products. Arbuscular mycorrhizae (phylum Glomeromycota) form symbiotic relationships with over 80% of vascular plants. In return for carbon, these fungi improve plant health and tolerance to environmental stress. This symbiosis is over 400 million years old and there are currently over 200 known arbuscular mycorrhizae, with dozens of new species described annually. Metagenomic sequencing of native soil communities, from species-rich meadows to mangroves, suggests biologically diverse habitats support a variety of mycorrhizal species with potential agricultural, medical, and biotechnological applications. This review looks at the effect of mycorrhizae on plant metabolism and how we can harness this symbiosis to improve crop health. I will first describe the mechanisms that underlie this symbiosis and what physiological, metabolic, and environmental factors trigger these plant-fungal relationships. These include mycorrhizal manipulation of host genetic expression, host mitochondrial and plastid proliferation, and increased production of terpenoids and jasmonic acid by the host plant. I will then discuss the effects of mycorrhizae on plant root and foliar secondary metabolism. I subsequently outline how mycorrhizae induce three key benefits in crops: defense against pathogen and herbivore attack, drought resistance, and heavy-metal tolerance. I conclude with an overview of current efforts to harness mycorrhizal diversity to improve crop health through customized inoculum. I argue future research should embrace synthetic biology to create mycorrhizal chasses with improved symbiotic abilities and potentially novel functions to improve plant health. As the effects of climate change and anthropogenic disturbance increase, the global diversity of arbuscular mycorrhizal fungi should be monitored and protected to ensure this important agricultural and biotechnological resource for the future.

Integrating Ontology into Ethnobotanical Research

Abstract: The title of this special section of the Journal of Ethnobiology, which grew out of a conference of the same name held at the University of Oxford in 2014, is intentionally provocative, immediately inspiring a number of questions: What might it mean to look at human-plant relations “ontologically”? What, indeed, is an “ontology,” and how does it relate to plants? Can the field of ethnobiology fruitfully engage with theoretical movements in the social sciences and humanities that advocate an ontological approach to human-nonhuman relations? In the epoch of the Anthropocene—and in light of the realization that the activity of human beings alters not only local ecosystems and the constitution of the atmosphere, but also the geological and tectonic foundations of the planet—how might human-plant relations be re-conceptualized and theorized? Further still, how can the relation between theory and practice be reformulated in light of these challenges? In this special section, we grapple with these difficult questions while remaining grounded in the interdisciplinary research concerning people and plants presented by our contributors. This preface serves to introduce the core concepts and questions discussed in the following articles, while providing some tools (including key bibliographic references) to aid in understanding. The last decade in the social sciences might be termed the Age of Ontology. The fervent adoption of this philosophical concept across a range of disciplines including anthropology, archaeology, information science, and science and technology studies (STS) has been heralded as signaling a paradigm shift (Carrithers et al. 2010; Henare et al. 2007). Ontology, of course, is a foundational area of enquiry in philosophy, where it refers to the study of the nature of being and reality. In the process of its experimental transposition into other disciplines, the meaning of the term has become increasingly kaleidoscopic to the extent that it defies generalization or definition (see Ellen, this issue). This intellectual moment has retroactively been given the epithet “the Ontological Turn,” a term that refers to a fragmented collection of philosophies with no cohesive vision but united by certain family resemblances (Pedersen 2012; Viveiros de Castro 2015). These approaches tend to

Species composition determines forage quality and medicinal value of high diversity grasslands in lowland England

Abstract: Current intensified livestock production threatens global biodiversity and food security. Increasing the use of semi-natural, species-rich grasslands for grazing and hay-making could serve as a way to bridge biodiversity conservation and livestock production but we know little about the nutritional composition of native grasslands. To determine the effect of grassland biodiversity on forage quality and the potential benefits and limitations of using conservation grasslands for agriculture, I conducted ecological and ethnobotanical research at 30 grassland sites in Oxfordshire, England. Species-richness and composition increased forage dry matter, sugar, and Phosphorus (P) content. Forage from species-rich grasslands contained up to 27% more protein, 56% more Phosphorus (P), 106% more Potassium (K), and 183% more Calcium (Ca) than cereals and conventional hay and met the nutritional requirements of beef cattle, sheep, and horses. Farmers and graziers valued species-rich grasslands were (1) the medicinal effect of specific grassland plants on livestock, (2) affordability, (3) the resilience of species-rich grasslands to drought and flooding, (4) conservation, and (5) marketability of pastoral products. The main factors inhibiting the (continued or increased) agricultural use of species-rich grasslands were restrictions on time of grazing, restrictions on time of hay-cut, and reduced grassland yield and forage quality due to recent increases in invasive plants. More flexible agro-environmental guidelines around species-rich grassland use are necessary to balance the agricultural as well as ecological value of these landscapes.

Horizontal 'gene drives' harness indigenous bacteria for bioremediation.

Abstract: Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60–99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

Biodiversity increases the resistance of ecosystem productivity to climate extremes

Abstract: It remains unclear whether biodiversity buffers ecosystems against climate extremes, which are becoming increasingly frequent worldwide. Early results suggested that the ecosystem productivity of diverse grassland plant communities was more resistant, changing less during drought, and more resilient, recovering more quickly after drought, than that of depauperate communities. However, subsequent experimental tests produced mixed results. Here we use data from 46 experiments that manipulated grassland plant diversity to test whether biodiversity provides resistance during and resilience after climate events. We show that biodiversity increased ecosystem resistance for a broad range of climate events, including wet or dry, moderate or extreme, and brief or prolonged events. Across all studies and climate events, the productivity of low-diversity communities with one or two species changed by approximately 50% during climate events, whereas that of high-diversity communities with 16–32 species was more resistant, changing by only approximately 25%. By a year after each climate event, ecosystem productivity had often fully recovered, or overshot, normal levels of productivity in both high- and low-diversity communities, leading to no detectable dependence of ecosystem resilience on biodiversity. Our results suggest that biodiversity mainly stabilizes ecosystem productivity, and productivity-dependent ecosystem services, by increasing resistance to climate events. Anthropogenic environmental changes that drive biodiversity loss thus seem likely to decrease ecosystem stability, and restoration of biodiversity to increase it, mainly by changing the resistance of ecosystem productivity to climate events.

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages.

Abstract: Host microbial cross-talk is essential to maintain intestinal homeostasis. However, maladaptation of this response through microbial dysbiosis or defective host defense toward invasive intestinal bacteria can result in chronic inflammation. We have shown that macrophages differentiated in the presence of the bacterial metabolite butyrate display enhanced antimicrobial activity. Butyrate-induced antimicrobial activity was associated with a shift in macrophage metabolism, a reduction in mTOR kinase activity, increased LC3-associated host defense and anti-microbial peptide production in the absence of an increased inflammatory cytokine response. Butyrate drove this monocyte to macrophage differentiation program through histone deacetylase 3 (HDAC3) inhibition. Administration of butyrate induced antimicrobial activity in intestinal macrophages in vivo and increased resistance to enteropathogens. Our data suggest that (1) increased intestinal butyrate might represent a strategy to bolster host defense without tissue damaging inflammation and (2) that pharmacological HDAC3 inhibition might drive selective macrophage functions toward antimicrobial host defense.

Metaproteomics: Studying functional gene expression in microbial ecosystems

Abstract: The recent availability of extensive metagenomic sequences from various environmental microbial communities has extended the postgenomic era to the field of environmental microbiology. Although still restricted to a small number of studies, metaproteomic investigations have revealed interesting aspects of functional gene expression within microbial habitats that contain limited microbial diversity. These studies highlight the potential of proteomics for the study of microbial consortia. However, the application of proteomic investigations to complex microbial assemblages such as seawater and soil still presents considerable challenges. Nonetheless, metaproteomics will enhance the understanding of the microbial world and link microbial community composition to function.

Absolute quantitation of microbiota abundance in environmental samples

Abstract: Microbial communities (microbiota) influence human and animal disease and immunity, geochemical nutrient cycling and plant productivity. Specific groups, including bacteria, archaea, eukaryotes or fungi, are amplified by PCR to assess the relative abundance of sub-groups (e.g. genera). However, neither the absolute abundance of sub-groups is revealed, nor can different amplicon families (i.e. OTUs derived from a specific pair of PCR primers such as bacterial 16S, eukaryotic 18S or fungi ITS) be compared. This prevents determination of the absolute abundance of a particular group and domain-level shifts in microbiota abundance can remain undetected. We have developed absolute quantitation of amplicon families using synthetic chimeric DNA spikes. Synthetic spikes were added directly to environmental samples, co-isolated and PCR-amplified, allowing calculation of the absolute abundance of amplicon families (e.g. prokaryotic 16S, eukaryotic 18S and fungal ITS per unit mass of sample). Spikes can be adapted to any amplicon-specific group including rhizobia from soils, Firmicutes and Bifidobacteria from human gut or Enterobacteriaceae from food samples. Crucially, using highly complex soil samples, we show that the absolute abundance of specific groups can remain steady or increase, even when their relative abundance decreases. Thus, without absolute quantitation, the underlying pathology, physiology and ecology of microbial groups may be masked by their relative abundance.

Arbuscular mycorrhizal fungi-induced mitigation of heavy metal phytotoxicity in metal contaminated soils: A critical review.

Abstract: The heavy metal pollution is a worldwide problem and has received a serious concern for the ecosystem and human health. In the last decade, remediation of the agricultural polluted soil has attracted great attention. Phytoremediation is one of the technologies that effectively alleviate heavy metal toxicity, however, this technique is limited to many factors contributing to low plant growth rate and nature of metal toxicities. Arbuscular mycorrhizal fungi (AMF) assisted alleviation of heavy metal phytotoxicity is a cost-effective and environment-friendly strategy. AMF have a symbiotic relationship with the host plant. The bidirectional exchange of resources is a hallmark and also a functional necessity in mycorrhizal symbiosis. During the last few years, a significant progress in both physiological and molecular mechanisms regarding roles of AMF in the alleviation of heavy metals (HMs) toxicities in plants, acquisition of nutrients, and improving plant performance under toxic conditions of HMs has been well studied. This review summarized the current knowledge regarding AMF assisted remediation of heavy metals and some of the strategies used by mycorrhizal fungi to cope with stressful environments. Moreover, this review provides the information of both molecular and physiological responses of mycorrhizal plants as well as AMF to heavy metal stress which could be helpful for exploring new insight into the mechanisms of HMs remediation by utilizing AMF.