Biology subjects

Hawkes, J.

Publications and source records attributed to Hawkes, J..

5 recordsLinked to original sources

bioRxiv2022

Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences on the diversity and function of heterotrophs are still not clear. Here we experimentally investigate heterotrophic bacteria in thirty-three freshwater model communities. We identified 34 different heterotrophs growing in ambient lake DOM with taxonomic affiliations matching abundant freshwater bacterioplankton. We further describe 25 different heterotrophs growing in the phycosphere of M. Aeruginosa and 6 heterotrophs growing on the DOM produced by M. Aeruginosa with taxonomic affiliation in accord to phycosphere heterotrophs. In our experiment we observed that heterotrophs that live in the phycosphere remove more dissolved organic carbon than abundant freshwater heterotrophs. Moreover, phycosphere heterotrophs have bigger genomes than abundant lake bacteria. Altogether of the 4224 chemical features that were resolved by LC-MS, only 1229 were seen in all three treatments. None of the common/shared compounds were removed across all the model communities, suggesting contrasting niches of the studied taxa. Altogether our study highlights how each model community, with its unique taxonomic assemblages and organotroph functioning is upkept by the chemodiversity of DOM.

ecology↗

bioRxiv2022

Abundance and expression of hgcAB genes and mercury availability jointly explain methylmercury formation in stratified brackish waters

Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgcA genes and MeHg across redox stratified water columns in the brackish Baltic Sea. We found that the abundance of hgcA genes and transcripts combined with the concentration of dissolved HgII-sulfide species were strong predictors of both HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. In establishing relationships between hgcA genes and MeHg, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen deficient zones.

ecology↗

bioRxiv2021

Fungal community composition along a gradient of permafrost thaw

Thermokarst activity at permafrost sites releases considerable amount of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi growing in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing a gradient of permafrost integrity. Samples were taken from the ponds surface water, the detritus and the sediment at the bottom of the ponds. These samples were extracted for total DNA, which was then amplified using primers targeting the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Surface water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.

ecology↗

bioRxiv2021

Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies

Inland waters receive and process large amounts of colored organic matter from the terrestrial surroundings. These inputs dramatically affect the chemical, physical, and biological properties of water bodies, as well as their roles as global carbon sinks and sources. To understand the complex changes associated with allochthonous inputs, experiments are needed. However, manipulative studies, especially at ecosystem scales, require large amounts of dissolved organic matter with optical and chemical properties resembling indigenous organic matter. Here we compared the chemical and biological impacts of two leonardite products (HuminFeed (HF) and SuperHume (SH)) and a freshly derived reverse osmosis concentrate of organic matter (RO) in a set of comprehensive mesocosm- and laboratory-scale experiments and analyses. The chemical properties of RO concentrate and the leonardite products were very different with leonardite products being low and RO being high in carboxylic functional groups. Light had a strong impact on the properties of leonardite products, including loss of color and increased particle formation. Furthermore, HF had drastic impacts on bacteria as light stimulated bacterial production and modified community composition, while dark conditions appeared to inhibit bacterial processes. While none of the browning agents inhibited the growth of the tested phytoplankton, Gonyostomum semen, leonardite products had detrimental effects on zooplankton abundance and Daphnia reproduction. We conclude that the effects of browning agents extracted from leonardite are in sharp contrast to those originating from terrestrially-derived DOM. Hence, they should be used with great caution in experimental studies on the consequences of terrestrial carbon for aquatic systems.

ecology↗

bioRxiv2020

Differential alteration of plant functions by homologous fungal candidate effectors

Rust fungi are plant pathogens that cause epidemics that threaten the production of important plant species, such as wheat, soy, coffee and poplar. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1 184 candidate effectors (CEs), however their functions are poorly known. In this study, we used Arabidopsis plants constitutively expressing CEs of Mlp to discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome of Arabidopsis plants expressing individually one of the 14 selected CEs and of a control line. We found 2 299 deregulated genes across the experiment. Among the down-regulated genes, the KEGG pathways "MAPK signaling pathway" and "Plant-pathogen interaction" were respectively over-represented in six and five of the 14 transgenic lines. Moreover, genes related to hormone response and defense were down-regulated across all transgenic lines are. We further observed that there were 680 metabolites deregulated in at least one CE-expressing transgenic line, with highly unsaturated and phenolic compounds enriched in up-regulated metabolites and peptides enriched among down-regulated metabolites. Interestingly, we found that transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors and their belonging to families may not be a good predictor of their impact on the plant. ImportanceRust fungi are plant pathogens that threaten the production of important crops, including wheat, soy, coffee and poplar. Effectors are used by pathogens to control the host, however in the case of Melampsora larici-populina, the causal agent of the poplar rust, and other rust fungi these proteins are poorly known. We used Arabidopsis plants expressing candidate effectors (CEs) of Mlp to better understand the interaction between this pathogen and its hosts. We found that expression of unrelated CEs led to similar patterns of gene and metabolite deregulation, while transgenic lines expressing CEs belonging to the same family showed different groups of different genes and metabolites deregulated. Thus, our results suggest that functional annotation of effectors based on sequence similarity may be misleading.

plant biology↗