Biology subjects

Hubert, J.

Publications and source records attributed to Hubert, J..

7 recordsLinked to original sources

bioRxiv2025

Echosounders for fish detection disturb harbour porpoises

The marine world is an acoustic world that has become noisier with the increasing diversity and intensity of human activities at sea. The harbour porpoise (Phocoena phocoena) is one of the best-studied cetaceans regarding hearing and responses to human-made underwater sound. The species is most sensitive to high frequencies, yet most impact studies have focused on relatively low-frequency sources. As such, the effects of high frequency sonar - including echosounders - remain largely unstudied, despite their widespread use on vessels for depth sounding, fish or object detection, and seabed mapping. We investigated the effects of scientific echosounder use on harbour porpoise occurrence using 13 multi-sensor mooring deployments in the southern part of the North Sea. Moorings operated for an average of 57 days, with split-beam scientific echosounders active for an average of 51 days, for 10 minutes every hour (5 min at 70 kHz, followed by 5 min at either 185-255 kHz or 70 kHz again). Porpoise acoustic presence was continuously monitored with C/F-PODs and additionally validated with hydrophone detections at four of the locations. Across all 13 sites, detections declined by 65- 79% during echosounder transmissions and returned to typical levels within [~]30 minutes after the echosounder stopped pinging. Despite this relatively quick recovery, there was no indication of habituation, as responses did not diminish across observation periods over six weeks of hourly exposure. Spatial effects appeared local, as no deterrent effect was observed at 2.5 km from the source. We believe that our findings have important implications for studies that investigate both harbour porpoise and fish presence to understand predator-prey interactions, but they should also raise concern about the potentially cumulative impact on sensitive cetaceans from the wide use of relatively high frequency sonar in offshore practices.

ecology↗

bioRxiv2025

Cultures of Tyrophagus putrescentiae experimentally infected with Cardinium and Wolbachia presented reduced fitness

Tyrophagus putrescentiae is a cosmopolitan pest of stored food and animal feed. Mite populations differ in their microbiome composition, resulting in variability in their fitness. Cultures of the stored-product mite T. putrescentiae are often singly infected by one of intracellular bacterial genera Cardinium and Wolbachia. No naturally occurring multi-infected (Cardinium/Wolbachia) cultures have been observed. Under laboratory conditions, we mixed two singly infected mite cultures, i.e., Cardinium-infected (5L and 5S) and Wolbachia-infected (5N and 5P) cultures, to obtain four experimental cultures (5LN, 5LP, 5SN and 5SP), each infected with each of the endosymbionts. Population growth was used as a fitness indicator, and PCR with specific primers for a single mite was used to identify the prevalence of Cardinium and Wolbachia in the parental and mixed cultures. The population growth of the experimental cultures was lower than that of the parents at the beginning of the experiment. After six months, 5SN and 5SP exhibited greater fitness than 5LP and 5LN. The population growth of the 5SN and 5SP cultures did not differ from that of the parental cultures 5P and 5S. Cardinium-infected mites prevailed in 6 cultures, Wolbachia-infected mites in 5 cultures, and asymbiotic individuals in 1 culture after six months. The proportion of Cardinium-infected individuals (45%) was greater than that of Wolbachia-infected individuals (25%), indicating that Cardinium had the ability to overcome Wolbachia. Although the cultures were multi-infected, doubly infected mites were rare (7%). These results suggest that Cardinium is responsible for cytoplasmic incompatibility in T. putrescentiae. The results revealed that the presence of the intracellular symbionts Cardinium and Wolbachia strongly influenced mite population growth in the experiments. These data support the importance of the microbiome in this pest.

zoology↗

bioRxiv2024

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective

Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19th century. The phylogeography of RYMV in East Africa was reconstructed from coat protein gene sequences (ORF4) of 335 isolates sampled over two million square kilometers between 1966 and 2020. Dispersal patterns obtained from ORF2a and ORF2b, and full-length sequences converged to the same scenario. The following imprints of rice cultivation on RYMV epidemiology were unveiled. RYMV emerged in the middle of the 19th century in the Eastern Arc Mountains where slash-and-burn rice cultivation was practiced. Several spillovers from wild hosts to cultivated rice occurred. RYMV was then rapidly introduced into the adjacent large rice growing Kilombero valley. Harvested seeds are contaminated by debris of virus infected plants that subsist after threshing and winnowing. Long-distance dispersal of RYMV is consistent (i) with rice introduction along the caravan routes from the Indian Ocean Coast to Lake Victoria in the second half of the 19th century, (ii) seed movement from East Africa to West Africa at the end of the 19th century, from Lake Victoria to the north of Ethiopia in the second half of the 20th century and to Madagascar at the end of the 20th century, (iii) and, unexpectedly, with rice transport at the end of the First World War as a troop staple food from the Kilombero valley towards the South of Lake Malawi. Overall, RYMV dispersal was associated to a broad range of human activities, some unsuspected. Consequently, RYMV has a wide dispersal capacity, its dispersal metrics estimated from phylogeographic reconstructions are similar to those of highly mobile zoonotic viruses. Author summaryRice yellow mottle virus (RYMV) poses a major threat to rice production in Africa. We explored through a multidisciplinary approach the links between the history of rice in East Africa since the second half of the 19th century and the spread of RYMV. The results illuminate the causes of RYMV diffusion. We show the role of long-distance caravan trade, the impact of the First World War and the consequences of seed exchange in the dispersal of RYMV. The paradoxical role of seeds in the spread of RYMV - which is vector transmitted and not seed transmitted - is explained in the light of rice biology and agronomy. Overall, this study reveals the wide range of transmission ways, some unexpected, in the dispersal of plant viruses. It also highlights the role of human transmission of pathogens, even vector-borne, and sheds light on the risk of transmission of RYMV and of other plant viruses from Africa to other continents.

evolutionary biology↗

bioRxiv2024

Secondary metabolites and their impact on symbiotic interactions in the ambrosia fungus Geosmithia eupagioceri

Ambrosia fungi colonize freshly dead trees, sequester nutrients, and serve as nutritional source for ambrosia beetles in exchange for dispersal. A key aspect of this symbiosis is the ability of fungi to colonize and dominate the wood around the beetle tunnels, forming a monospecific nutritional mycelium in the beetle gallery. Hypotheses for these dynamics include active beetle management, fungal inoculation priority, and the funguss chemical ecology facilitating resource capture and competition. The ecological role of allelochemicals produced by ambrosia fungi is unknown, although they may suppress microbes while being harmless to beetles, which has potential medical or food technology applications. This study presents a comprehensive analysis of secondary metabolites from the ambrosia fungus Geosmithia eupagioceri (Ascomycota: Hypocreales). Eight extracellular compounds were identified in vitro: 5-hydroxymethyl-2-furancarboxylic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 3,4-dihydroxybenzoic acid, 4-hydroxyphenylacetic acid (4-HPA), 4-HPA methyl ester, tyrosol, and thymine. Most compounds show cross-taxon activity, suppressing the growth of bacteria, fungi, a nematode, and a mite. We have shown that often overlooked chemically simple compounds may have activities leading to increased fitness of beetle hosts, including previously unconsidered activity against mites and nematodes. For the first time, we point out that these compounds also have the previously unconsidered potential to modulate the physiology of their producer (by inducing symbiotic morphology by quorum sensing mechanisms), the beetle host and associated microbes through synergism. Furthermore, we have shown that the ambrosia fungi have biotechnological potential in the search for growth suppressors of microorganisms and invertebrates, not toxic to humans. IMPORTANCEBark and ambrosia beetles and their microbial symbionts play crucial roles in forest ecosystems by aiding in the decomposition of dead trees, nutrient cycling, and habitat creation. However, they can cause extensive damage to both natural and planted forests by killing trees. Our study has led to a fundamental shift in the understanding of interactions between beetle symbiotic fungi and the environment, mediated by secondary metabolites. Newly, we show that these substances can not only be antimicrobial but also suppress the growth of mites, nematodes, but also can modulate the physiology of the producer fungus and potentially the host beetle and associated microbes. Our study, although conducted on a relatively artificial system with the need for validation on other lineages of ambrosia fungi, suggests entirely new research directions in the understanding of bark beetle holobiont and ambrosia beetles.

microbiology↗

bioRxiv2023

Predicting Blomia tropicalis allergens using a multiomics approach

The domestic mite Blomia tropicalis is a major source of allergens in tropical and subtropical regions. Despite its great medical importance, the allergome of this mite is not sufficiently studied. Only 14 allergen groups have been identified in B. tropicalis so far, even though early radioimmunoelectrophoresis techniques (27 uncharacterized allergen complexes) and comparative data based on 40 allergen groups officially recognized by WHO/IUIS in domestic astigmatid mites, suggest that a large set of additional allergens may be present. Here, we use a multiomics approach to assess the allergome of B. tropicalis using genomic, transcriptomic sequence data, and a highly sensitive protein abundance quantification. Out of 14 known allergen groups, we confirmed 13 (one WHO/IUIS allergen, Blo t 19, was found to be a contaminant originated from a nematode) and identified 16 potentially novel allergens using sequence similarity. These data indicate that B. tropicalis shares 27 known/deduced allergen groups with pyroglyphid house dust mites (genus Dermatophagoides). Among them, five allergen-encoding genes were highly expressed at the transcript level: Blo t 1, Blo t 5, Blo t 21 (known), Blo t 15, and Blo t 18 (predicted). However, at the protein level, a different set of most abundant allergens was found: Blo t 2, 10, 11, 20 and 21 (mite bodies) or Blo t 3, 4, 6 and predicted Blo t 13, 14 and 36 (mite feces). We show the use of an integrated omics method to identify and predict an array of mite allergens and advanced, label-free proteomics to determine allergen protein abundance. Our research identifies a large set of novel putative allergens and shows that expression levels of allergen-encoding genes may not be strictly correlated with the actual allergenic protein abundance in the mite bodies.

molecular biology↗

bioRxiv2020

Rhamnolipids and their 3-(3-hydroxyalkanoyloxy)alkanoic acid precursors activate Arabidopsis innate immunity through two independent mechanisms

Plant innate immunity is activated upon perception of invasion pattern molecules by plant cell-surface immune receptors. Several bacteria of the genera Pseudomonas and Burkholderia produce rhamnolipids (RLs) from L- rhamnose and (R)-3-hydroxyalkanoate precursors (HAAs). RL and HAA secretion is required to modulate bacterial surface motility, biofilm development, and thus successful colonization of hosts. Here, we show that the lipidic secretome from the opportunistic pathogen Pseudomonas aeruginosa mostly comprising RLs and HAAs stimulates Arabidopsis immunity. We demonstrate that HAAs are sensed by the bulb-type lectin receptor kinase LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION/S-DOMAIN-1-29 (LORE/SD1-29) that also mediates medium-chain 3-hydroxy fatty acid (mc-3-OH-FA) perception in the plant Arabidopsis thaliana. HAA sensing induces canonical immune signaling and local resistance to plant pathogenic Pseudomonas infection. By contrast, RLs trigger an atypical immune response and resistance to Pseudomonas infection independent of LORE. Thus, the glycosyl moieties of RLs, albeit abolishing sensing by LORE, do not impair their ability to trigger plant defense. In addition, our results show that RL-triggered immune response is affected by the sphingolipid composition of the plasma membrane. In conclusion, RLs and their precursors released by bacteria can both be perceived by plants but through distinct mechanisms. SignificanceActivation of plant innate immunity relies on the perception of microorganisms through self and nonself elicitors. Rhamnolipids and their precursor HAAs are exoproducts produced by beneficial and pathogenic bacteria. They are involved in bacterial surface dissemination and biofilm development. As these compounds are released in the extracellular milieu, they have the potential to be perceived by the plant immune system. Our work shows that both compounds independently activate plant immunity. We demonstrate that HAAs are perceived by the receptor protein kinase LORE. By contrast, rhamnolipids are not senses by LORE but activate a non-canonical immune response affected by the sphingolipid composition of the plant plasma membrane. Thus, plants are able to sense bacterial molecules as well as their direct precursors to trigger a distinct immune response.

plant biology↗

bioRxiv2018

Influence of Arm Swing on Cost of Transport during Walking

Normal arm swing plays a role in decreasing the cost of transport during walking. However, whether excessive arm swing can reduce the cost of transport even further is unknown. Therefore, we tested the effects of normal and exaggerated arm swing on the cost of transport in the current study. Healthy participants (n=12) walked on a treadmill (1.25 m/s) in seven trials with different arm swing amplitudes (in-phase, passive restricted, active restricted, normal, three gradations of extra arm swing), while metabolic energy cost and the vertical angular momentum (VAM) and ground reaction moment (GRM) were measured.\n\nIn general, VAM and GRM decreased as arm swing amplitude was increased, except for in the largest arm swing amplitude condition. The decreases in VAM and GRM were accompanied by a decrease in cost of transport from in-phase walking (negative amplitude) up to a slightly increased arm swing (non-significant difference compared to normal arm swing). The most excessive arm swings led to an increase in the cost of transport, most likely due to the cost of swinging the arms. In conclusion, increasing arm swing amplitude leads to a reduction in vertical angular moment and ground reaction moments, but it does not lead to a reduction in cost of transport for the most excessive arm swing amplitudes. Normal or slightly increased arm swing amplitude appears to be optimal in terms of cost of transport in young and healthy individuals.\n\nSUMMARY STATEMENTExcessive arm swing reduces the vertical angular momentum and ground reaction moment, but not necessarily the energetic cost of transport.

neuroscience↗