Species Relative Abundance Research Articles

Урожайність молоді риб прибережних ділянок р. Дністер у межах Івано-Франківської області

Purpose. Taking into account the unique ichthyological complex of the upper course of the Dniester River, the studies should be directed both at the structure of the ichthyofauna and at its quantitative parameters of the species structure, and fish with a special conservation status need special attention. Therefore, the purpose of our work was to determine the peculiarities of the current structural and functional organization of the ichthyocenosis of the Dniester River within the Ivano-Frankivsk region. Methodology. Quantitative assessment of fish juveniles was carried out using the area method. Fish juveniles were identified to the species level using A.F. Koblytska and Yu.V. Movchan identification keys. All fish, after some measurements, were released to the place where they were caught in an undamaged state and alive. After identification of fish species with a special conservation status, which were trapped into the fishing gear, they were immediately returned to their habitat without removing them from water. Findings. Fourteen fish species were observed in the community of fish juveniles on the nearshore areas of the Dniester River in the Ivano-Frankivsk region. According to the data of the analysis, following relative abundances of juvenile fish species were observed: vyrezub (40% of the total abundance), bleak (23% of the total abundance) and vimba (18% of the total abundance). The total relative abundance of fish juveniles with special conservation status in the total catch was 68%, which suggested the need to create additional zones in order to increase conservation measures. Given the high share of fish species with special conservation status, the assessment of species biodiversity in terms of biotope similarity is important. The area of Mariyampil village and floodplain coastal areas were characterized by the highest biodiversity in terms of species composition of ichthyofauna among the studied biotopes. The highest abundance of fish juveniles in absolute values was recorded in the mouth areas of the rivers, but its high values were achieved due to the juveniles of vyrezub. Also, this studied nearshore area was not characterized by a high biodiversity of ichthyofauna, which was confirmed by the Shannon-Weaver index at the level of 1.74. According to the results of our study, it can be stated that the nearshore areas of the mouth part of the rivers are important and unique for the formation of ichthyocenosis specifically for the vyrezub. Thus, it can be concluded that all analyzed stations were characterized by the presence of vyrezub, which allows classifying the studied area as important in terms of environmental protection. In view of the prevalence of juvenile vyrezub within the studied areas, protective measures are more important, which are aimed not only at ensuring control over the state of aquatic biological resources, but also at the organization of artificial replenishment of natural localities and the creation of new populations of this species with their purposeful acclimatization in specially selected ecological conditions of the water body. Originality. For the first time, the yield of fish juveniles in the nearshore areas of the Dniester River within the Ivano-Frankivsk Region was analyzed. The obtained data will be used to solve the problem of the preservation of species diversity and the abundance of fish species, which are valuable in terms of environmental protection. Practical value. As a result of the assessment of the current state of the ichthyofauna of the Dniester River within the limits of the Ivano-Frankivsk region, data were obtained regarding the natural localities of rare and endangered fish species in the specified area. Keywords: ichthyofauna, Dniester River, protected species, natural locality.

Modelling the effects of potential climate change on the dynamics of multi-species mountain pastures: A case study in Gran Paradiso National Park, Italy

CONTEXTPasture dynamics of Alpine areas are linked to the complex cryospheric hydrology of Alpine catchment and to the interspecies competition, which are in turn expected to change remarkably under prospective global warming scenarios. OBJECTIVEThis study aimed at assessing the impact of climate change on the productivity of mountain pastures in the Gran Paradiso National Park (Italy). METHODSThe hydrological model Poli-Hydro was used, coupled with the Poli-Pasture model, able to simulate pasture growth, which was further integrated with CoSMo model to consider interspecific competition. Two (competing) species were chosen for low altitude LowAlt areas (below 1800 m asl), Trifolium alpinum and Dactylis glomerata, and two for high altitude HighAlt areas (above 1800 m asl), Festuca rubra and Nardus stricta. Model tuning and evaluation were performed against estimates of leaf area index (LAI), derived from satellite imagery during 2005–2019. Then, climate change impacts were projected until 2100 by considering four IPCC AR6 scenarios and six GCMs. Target variables included a set of agroclimatic indices, LAI and pasture yield. RESULTS AND CONCLUSIONSDue to the projected increase in temperatures during the XXI century, a measurable potential increase in productivity would be expected, especially in the highest areas (up to +97% by 2050, and + 123% by 2100 for the SSP5–8.5 scenario). The relative abundance of pasture species appears to remain mostly stable; at most, the species with higher fodder value even increases slightly. This suggests that a loss in the overall quality of biomass should not occur. These results provide preliminary evidence for the potential development of livestock farming, and thus of a relevant part of the economy in the valleys, at higher altitudes than now. However, to a certain extent pasture performance could be threatened by the projected reduction in summer rainfall, and possibly spreading of pests with increasing temperature. SIGNIFICANCEThe results obtained here could be useful for policy makers, and scientists in the field of pasture/grasslands management, to depict scenarios of future productivity, and to support redefinition of periods, and areas designated for grazing activities in the mountains.

Using plant functional types to predict the influence of fire on species relative abundance

Fire influences plant survival, reproduction, and establishment. Consequently, plants exhibit fire-related traits. Grouping species with similar traits into Plant Functional Types (PFTs) enables predictions of fire–related change based on ecological mechanisms. However, if PFTs are to advance conservation decision-making, we must know if predictions are robust. We developed a PFT approach to predict how species relative abundance changes as a function of time since fire, and tested predictions empirically. First, we used trait databases and ecological knowledge to assign species into PFTs based on fire-related mechanisms. Second, we developed graphical predictions of fire-related change in relative abundance. Third, we collected data on species relative abundance at 57 sites, across an 81–year post–fire chronosequence. Finally, we tested predictions using non–linear regression models. Predictions of the direction of changes in relative abundance (increase or decrease from 0 to 81 years since fire) were correct for 18 of 24 species modelled. Predictions of the shape of changes in relative abundance were not as accurate, but still useful: 13 out of 24 species showed ‘excellent’ conformity with shape predictions, 7 ‘good’ conformity, and 4 ‘poor’. Broader functional groupings commonly used in ecology, such as facultative resprouter, inadequately captured changes in relative abundance. An advance of this study is that the direction and trajectory of changes in species relative abundance can be predicted using deductive PFTs that represent population processes. This suggests PFTs can be used to generalize fire responses across species that share similar traits, and thus inform biodiversity conservation and management.

Abstract 2800: Shotgun metagenomics of COPD-associated lung cancer tissue microbiome

Abstract The gut microbiome plays a crucial role in the development of multiple chronic diseases. Several solid tumors including lung cancer are also implicated in the gut microbiome in cancer initiation and progression, possibly affecting signaling pathways in the tumor microenvironment. However, the microbiome in the peripheral lung tissue is unexplored and their relationship to the lung tumor microenvironment is still unknown. Thus, to explore the relationship between the microbiome and the tumor microenvironment of lung cancer, we performed shotgun metagenomic sequencing of the lung cancer tissue, especially in lung cancer patients accompanied by chronic obstructive pulmonary disease (COPD). We confirmed the presence of a diverse microbiome in peripheral lung cancer tissue. Next, we focused on individual species. We observed significant differences in the relative abundance of several species between COPD and non-COPD patients, and cancer and non-cancer tissue. Then, we focused on the metagenomic diversity between samples. The number of species in COPD patients and cancer tissue were decreased. And the bacterial total abundance in each sample were observed similar trend. On the other hand, alpha diversity in each sample were showed different trend to them. In the analysis of beta diversity using Principal Coordinate Analysis (PCoA), clusters were formed in each group. These findings suggest that microbiome imbalance known as dysbiosis in the peripheral lung tissue may affect the tumor microenvironment resulting in cancer progression. Citation Format: Atsushi Matsuoka, Kazuhiko Shien, Shuta Tomida, Daisuke Mizuno, Masayoshi Ohki, Ryo Yoshichika, Tomohiro Higashihara, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Ken Suzawa, Hiromasa Yamamoto, Shinichi Toyooka. Shotgun metagenomics of COPD-associated lung cancer tissue microbiome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2800.

Abstract 6681: Altered microbial community stability and increases in circulating B cells are associated with the development of severe immune related adverse events during ICI-immunotherapy

Abstract Background: Immune related adverse events (irAEs) are a major hurdle to the success of immune checkpoint inhibitor (ICI) immunotherapy. There is increasing evidence that the gut microbiota influences irAE development, however the microbe-immune crosstalk underpinning this remains cryptic. Methods: Paired pre- & post-treatment (baseline/week 6) stool samples from 129 Australian and Dutch melanoma patients treated on trial with neo-adjuvant combination anti-PD1/anti-CTLA4 immunotherapy were analyzed with 16S rRNA gene sequencing. Matched PBMCs at both timepoints were analyzed using mass cytometry (n=71). Results: ICI immunotherapy resulted in changes in the relative abundance of specific bacterial groups in the faecal microbiota, however the microbial community as a whole remained relatively stable. In particular enhanced oralization of the gut microbiome was observed with treatment, including a significant increase in the relative abundance of oral Streptococcus species in the gut (P=0.0004). These changes were particularly evident in patients whose microbial communities were Bacteroidaceae (Ba)-dominated at baseline, and those who developed severe (grade 3+) irAEs. Indeed, Ba-dominated microbiomes were linked with comparatively higher rates of severe irAEs compared to patients with Ruminococcaceae (Ru)-dominated gut microbiomes (P= 0.0440). Furthermore, Ba patients developed severe irAEs earlier during treatment, prior to week 6 (P=0.0016). A significant reduction in transitional B cells (CD24+ CD38hi CD27-) (P<0.0001) and an increase in activated B cells subsets (CD27- CD38- CD24- populations) (P=0.0022) were observed between baseline and week 6 across all patients who developed or went on to develop severe irAEs. Most notably, Ba patients who developed early, severe irAEs specifically had significantly higher frequencies of overall circulating B cells (P=0.0018) and lower frequencies of ICOS+ Tregs at week 6 post treatment (P=0.0005), which was not observed in Ru-dominated irAE patients. Conclusions: Higher risk of early, severe irAEs were associated with Bacteroidaceae-dominated gut microbiomes, reduced microbial community stability, and increases in activated circulating B cells during treatment. We postulate that differing baseline microbial community assemblages are associated with altered pre-established intestinal homeostasis influencing the likelihood of irAE development. Together, the data highlights a potential relationship between B cells, the gut microbiota and irAE development which may point to early steps in the induction of irAEs during ICI immunotherapy. Citation Format: Rebecca C. Simpson, Erin R. Shanahan, Ines P. Silva, Irene L. Reijers, Judith M. Versluis, Alexander M. Menzies, Gonzalez Maria, Umaimainthan Palendira, James S. Wilmott, Christian Blank, Richard A. Scolyer, Georgina V. Long. Altered microbial community stability and increases in circulating B cells are associated with the development of severe immune related adverse events during ICI-immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6681.

The Relationship between the Edge Density of the Forest Fragments and the Tree Species Richness in the Detached Fragments of Kakamega Forest.

Purpose: The theoretical approach guiding this study was based on the Island Biogeography Theory. The purpose of this study was to assess the influence of the edge density of the forest fragments on tree species richness.
 Methodology: The study adopted a cross-sectional correlational research design. Proportionate random sampling was used. A sample of 30 plots each measuring 2m by 2m was established randomly in the fragments (0-200m from the edge towards the interior);Malava: Kisere: Ikuywa in that order for field sampling and measurements. Data was collected using tools such as measuring tapes,metre rule,GPS 64s Garmain and suunto inclinometer. A total of 39 species of trees were recorded from the three fragments with Funtumia africana being recorded as the most abundant species.
 Findings: The findings show 83%, 85%, and 92% variation of tree species richness in. Malava (r2 = 0.83), Kisere (r2 = 0.85) and Ikuywa (r2 = 0.92) in that order can be explained by the edge density of the fragments. The edge density also explained 87%, 94% and 94% variation of tree species relative abundance in Malava (r2 = 0.87), Kisere (r2 = 0.94) and Ikuywa (r2 = 0.94) in that order.
 Unique Contributor to Theory, Policy and Practice: It was concluded that tree species richness and tree species abundance in the detached portions of Kakamega forest were dominantly influenced by forest fragment total edge length and fragment edge density. For us to conserve more tree species we recommend maintenance of the total edge length of the fragments above 15km with edge density (3.413.79m\m2) in order to maintain high tree species richness and tree species relative abundance.

Forest types outpaced tree species in centroid-based range shifts under global change

IntroductionMounting evidence suggests that geographic ranges of tree species worldwide are shifting under global environmental changes. Little is known, however, about if and how these species’ range shifts may trigger the range shifts of various types of forests. Markowitz’s portfolio theory of investment and its broad application in ecology suggest that the range shift of a forest type could differ substantially from the range shifts of its constituent tree species.MethodsHere, we tested this hypothesis by comparing the range shifts of forest types and the mean of their constituent species between 1970–1999 and 2000–2019 across Alaska, Canada, and the contiguous United States using continent-wide forest inventory data. We first identified forest types in each period using autoencoder neural networks and K-means cluster analysis. For each of the 43 forest types that were identified in both periods, we systematically compared historical range shifts of the forest type and the mean of its constituent tree species based on the geographic centroids of interpolated distribution maps.ResultsWe found that forest types shifted at 86.5 km·decade-1 on average, more than three times as fast as the average of constituent tree species (28.8 km·decade-1). We showed that a predominantly positive covariance of the species range and the change of species relative abundance triggers this marked difference.DiscussionOur findings provide an important scientific basis for adaptive forest management and conservation, which primarily depend on individual species assessment, in mitigating the impacts of rapid forest transformation under climate change.

PDA-Fe3O4 decorated carbon felt anode enhancing electrochemical performance of microbial fuel cells: Effect of electrode materials on electroactive biofilm

Anode modification is an effective strategy for enhancing the electrochemical performance of microbial fuel cell (MFC). However, the impacts of the modified materials on anode biofilm development during MFC operation have been less studied. We prepared a novel PDA-Fe3O4-CF composite anode by coating original carbon felt anode (CF) with polydopamine (PDA) and Fe3O4 nanoparticles. The composite anode material was characterized by excellent hydrophilicity and electrical conductivity, and the anodic biofilm exhibited fast start-up, higher biomass, and more uniform biofilm layer after MFC operation. The MFC reactor assembled with the composite anode achieved a maximum power density of 608 mW m−2 and an output voltage of 586 mV, which were 316.4% and 72.4% higher than the MFC with the original CF anode, respectively. Microbial community analysis indicated that the modified anode biofilm had a higher relative abundance of exoelectrogen species in comparison to the unmodified anode. The PICRUSt data revealed that the anodic materials may affect the bioelectrochemical performance of the biofilm by influencing the expression levels of key enzyme genes involved in biofilm extracellular polymer (EPS) secretion and extracellular electron transfer (EET). The growth of the anodic biofilm would exert positive or negative influences on the efficiency of electricity production and electron transfer of the MFCs at different operating stages. This work expands the knowledge of the role that anodic materials play in the development and electrochemical performance of anodic biofilm in MFCs.

Deep learning enables early stage prediction of preterm birth using vaginal microbiota

Graphical abstract Abstract Objective Preterm birth (PTB) is one of the leading issues concerning infant health and is a problem that plagues all parts of the world. Vaginal microbial communities have recently garnered attention in the context of PTB; however, the vaginal microbiome varies greatly from individual to individual, and this variation is more pronounced in racially, ethnically, and geographically diverse populations. Additionally, microbial communities have been reported to evolve during the duration of the pregnancy, and capturing such a signature may require higher, more complex modeling paradigms. In this study, we develop a neural controlled differential equation (CDE)-based framework for identifying early PTBs in racially diverse cohorts from irregularly sampled vaginal microbial abundance data. Methods We obtained relative abundances of microbial species within vaginal microbiota using 16S rRNA sequences obtained from vaginal swabs at various stages of pregnancy. We employed a recently introduced deep learning paradigm known as ‘neural CDEs’ to predict PTBs. This method, previously unexplored, analyzes irregularly sampled microbial abundance profiles in a time-series format. Results Our framework is able to identify signatures in the temporally evolving vaginal microbiome during trimester 2 and can predict incidences of PTB (mean test set ROC–AUC = 0.81, accuracy = 0.75, F1 score = 0.71) significantly better than traditional ML classifiers, thus enabling effective early-stage PTB risk assessment. Conclusion and significance Our method is able to differentiate between term and preterm outcomes with a substantial accuracy, despite being trained using irregularly sampled microbial abundance profiles, thus overcoming the limitations of traditional time-series modeling methods.

Integrated metabolome–metagenome analysis provides new insights into the impacts of sea cucumber (Apostichopus japonicus) aestivation on marine sediment composition

To explore the impacts of sea cucumber aestivation on sediment composition, sediments were sampled from aestivation sites and non-aestivation sites of a commercial Apostichopus japonicus culture pond, and metabolome–metagenome integrated analysis was performed. The results showed that 1) there was no significant difference in the microbial composition of sediments between aestivation and non-aestivation sites, but the relative abundances of some bacterial species changed slightly (especially pathogenic and spoilage species); 2) altered average relative abundances of potential host bacteria of antibiotic resistance genes (ARGs) were observed; 3) compared with non-aestivation site sediments, decreased average absolute abundances of two ARGs (tetW and floR) and increased average absolute abundance of one ARG (tetM) were observed in aestivation site sediments; and 4) a total of 74 significantly differentially expressed metabolites (SDMs) were identified in aestivation sites compared with non-aestivation sites. Four SDMs were closely correlated with antibacterial activity and bacterial physiology. All data observed in this study indicate that sea cucumber aestivation does not affect sediment microbial composition but does influence the relative abundances of some bacteria species; in addition, tetM might be considered a key indicator for monitoring and indicating ARG transfer or the sediment status of sea cucumber culture ponds during aestivation. In conclusion, the observations of this study enrich our knowledge of the impacts of the physiological behavior of marine ecosystem inhabitants on their ecosystem and provide novel insights for the management of aquaculture activities.

Microbiome changes through the ontogeny of the marine sponge Crambe crambe

BackgroundPoriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding.ResultsUsing 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics.ConclusionsThese findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.

Nitrite nitrogen stress disrupts the intestine bacterial community by altering host-community interactions in shrimp

Environmental stress can disrupt the intricate interactions between the host and intestine microbiota, thereby impacting the host health. In this study, we aimed to elucidate the dynamic changes in the bacterial community within shrimp intestines under nitrite nitrogen (nitrite-N) stress and investigate potential host-related factors influencing these changes. Our results revealed a significant reduction in community diversity within the intestine exposed to nitrite-N compared to control conditions. Furthermore, distinct differences in community structures were observed between these two groups at 72 h and 120 h post-stress induction. Nitrite-N stress also altered the abundances of some bacterial species in the intestine dramatically. It is noteworthy that, in comparison to the 72 h, intestine bacterial community structure of stressed shrimp exhibited a significantly higher degree of dispersion after 120 h of nitrite-N stress when compared to control shrimp, and the relative abundance of numerous bacterial species experienced a substantial decrease or even reached 0 %. Moreover, it led to a reduction in bacterial community interactions and decreased competitiveness within the intestine microbiota. Notably, the influence of bacterial community assemblies in the shrimp intestine shifted from a stochastic process to a deterministic one after 24 h and 72 h of nitrite-N stress, returning to a stochastic process at 120 h. We further observed a close association between this phenomenon and host's response to nitrite-N stress. Expression levels of differentially expressed genes in the intestinal tissue significantly impact the intestine bacterial diversity and abundance of species. In particular, the significant decline in bacterial diversity and abundances of quite a few species in intestine was attributed to the up-regulation of peritrophin-48-like. Overall, nitrite-N stress indeed disrupted the intestine microbiota and changed the host-microbiota interactions of shrimp. This study offered novel insights into environment-host-microbiota interactions and also provided practical guidance for promoting healthy shrimp cultivation practices.

An exploratory analysis of the structure of tetranychid and phytoseiid assemblages in walnut orchards in California.

Spider mites were considered secondary pests of walnut production in California, under the control of phytoseiid predators. Due to increased importance as walnut pests in recent decades there is renewed interest in the structure and function of the associated phytoseiid assemblage. In this study we report the results from a 3 year survey of the tetranychid and phytoseiid assemblages in walnut orchards in the Central Valley of California. The survey was conducted to determine the range and dominance of web-spinning Tetranychus species present, to investigate the species richness and dominance of the phytoseiid species present, and to explore whether patterns of variation in the relative abundance of phytoseiid species could be explained by one or more explanatory variables. Tetranychus urticae was the dominant spider mite in all growing regions and years with T. pacificus and T. turkestani also present in orchards in the southern San Joaquin Valley. Phytoseiid species richness declined with latitude among the three walnut growing regions and of the 13 species found Amblyseius similoides, Euseius stipulatus, Galendromus occidentalis and Typhlodromus caudiglans were the most abundant and widespread species present. Mean proportional abundance significantly increased from early (mid May-July) to late (August-mid October) season and from southern to northern growing regions for Type II and IV predators, but significantly decreased from early to late season and from southern to northern growing regions for Type III predators. The mean proportional abundance of Type II predators, particularly G. occidentalis, significantly increased and that of Type III predators significantly decreased with mean Tetranychus density in individual orchards. The current survey provides a more in-depth analysis of mite assemblages in walnut orchards in California and can be used to better inform adaptive management strategies for integrated mite management in the future.

Abrupt intensification of AMOC and monsoonal winds during mid-MIS4 (Heinrich Event 6) in the western Arabian Sea

In the Arabian Sea (AS), higher organic matter preservation and biological productivity are observed during the summer due to strong southwest monsoonal winds. Centennial and millennial-scale fluctuation in the geochemical and relative abundance of foraminifera species are widely used to study the past preservation and productivity variation reconstruction in the Western Arabian Sea (WAS). The sediment records from the AS also show similarities with the North Atlantic and Greenland mainly during Heinrich events (HEs) which is related to the atmospheric and oceanic teleconnections of the AS with the higher latitude climate perturbations. In this context, we used a sediment core VM3504-PC from the WAS to understand the long-term changes in productivity and organic matter preservation using Globigerina bulloides (G. bulloides) relative abundance, total organic carbon (TOC) content, and calcium carbonate (CaCO3) wt%. The TOC and G. bulloides shows a positive correlation, while significantly negative correlation is recorded in the TOC % and CaCO3 wt% datasets during interglacial periods (MIS5e-b, MIS3, and MIS1). Our results show evidence of CaCO3 dissolution and intense summer monsoon induced upwelling related productivity in core location during interglacial periods (MIS5e), based on higher relative abundance of G. bulloides (%), higher TOC content, and lower CaCO3 wt%. Interestingly, higher preservation of organic matter and increased productivity/nutrient concentration during mid-MIS4 suggesting stronger upwelling/winter convective mixing together with higher aeolian transport from adjacent landmasses. The abrupt weakening in the Atlantic Meridional Overturning Circulation (AMOC) synchronized with low productivity due to weak monsoon during HEs except for H6 and H4 in the tropical Indian Ocean. The H6 coincides with mid-MIS4 is showing abnormal preservation. Thus, AMOC and the summer monsoon significantly regulate primary productivity in the WAS. It is interesting to note that possibly well‑oxygenated deep-water masses do not penetrate up to surface water and/or ballistic effect (indicated by moderate sedimentation rate), preventing organic matter degradation on the seafloor during mid-MIS4.

Larval fish community in the Bay of Whales (eastern Ross sea): Species composition, relative abundance and spatial distribution

Early life stages of fish represent a key component in the food chain of the pelagic ecosystem of the Southern Ocean, connecting producer trophic levels to those of higher predators. Pelagic larvae and early juveniles of notothenioid fishes overwhelmingly dominate the ichthyoplankton community living on the continental shelf. Scientific research surveys targeting early life stages of fish in the pelagic realm have been mainly carried out in the western Ross Sea, whereas the eastern side can be considered unexplored. As source of high primary production, the presence and timing of formation of wide ice-free areas throughout the year in the Ross Sea play a fundamental role in structuring larval fish community. The Ross Ice Shelf Polynya (RISP) is a large coastal polynya, which is driven and maintained by local prevailing winds and oceanic currents. In the present study, we report the first data on species composition, relative abundance and spatial distribution of larval fish community found off the Bay of Whales in the eastern Ross Sea. As reported for other areas of the Ross Sea, the Antarctic silverfish Pleuragramma antarcticum was by far the most abundant species, followed by other nototheniids and channichthyids in smaller amounts. The huge abundance of P. antarcticum early larvae supports the hypothesis of a potential nursery area near the Bay of Whales. Present results strongly advocate for future investigations in these poorly known and remote areas.

140 High-resolution characterization of the gut microbiota of neonatal dairy calves using full-length 16S rRNA gene amplicon sequencing

Abstract The gut microbiota has a crucial role in preventing pathogen colonization and training the immune system. An imbalanced gut microbiota tends to induce calf diarrhea, which can lead to dehydration and metabolic acidosis. Therefore, it is urgent to identify critical factors that influence the establishment of gut microbiota in the early stages of development in dairy calves. Most previous research relied on short-read-based partial 16S rRNA gene amplicon sequencing to study calf microbiota, which has limited taxonomic resolution. The aim of our study is to obtain a species-level characterization of calf gut microbiota using long-read based full-length 16S rRNA gene amplicon sequencing and investigate the factors that affect the gut microbiota composition in the early stages of development in dairy calves. We collected fecal samples from the recto-anal junction of 25 Holstein-Angus crossed calves at d 4 and d 14 after birth. The calves were raised in individual outdoor hutches from birth and fed milk replacer twice daily. The gut microbiota was analyzed using full-length 16S rRNA gene amplicon sequencing on an Oxford Nanopore sequencer. The results revealed that the gut microbial diversity measured by Chao 1 (P < 0.001) and Shannon index (P < 0.001) significantly increased from d 4 to d 14. We identified 15 and 36 core bacterial species (prevalence ≥ 80%) in d 4 and d 14 gut microbiota, respectively, and both stages share 7 bacterial species: Bacteroides fragilis, Butyricicoccus pulicaecorum, Enterocloster bolteae, Escherichia coli, Lachnoclostridium sp YL32, Rumiococcus gnavus and Streptococcus equinus. The calf gut microbiota was dominated by Bacteroides fragilis (18%), Escherichia coli (13%), Ruminococcus gnavus (10%) and Butyricicoccus pulicaecorum (6%) species on d 4, and Megamonas rupellensis (18%) and Fusobacterium varium (6%) species (relative abundance > 5%) on d 14. Notably, we found a significant impact of hutch location on the composition of gut microbiota, particularly on d 4, but the impact was reduced on d 14. Moreover, there were 4 dystocia calves among the 25 calves, which had a significantly lower Shannon index (P = 0.046) compared with 4 paired normal calves of similar age and sex, and location balanced. In conclusion, this study provides a species-level resolution of gut microbiota for neonatal dairy calves and indicates a potential impact of dystocia on early microbiota development. Additionally, calf microbiota composition is influenced by environmental factors, likely the soil microbiota where hutches were located, with a more substantial effect on the microbiota at an earlier age.

Dynamic changes in the gut microbiota after bismuth quadruple therapy and high-dose dual therapy for Helicobacter pylori eradication.

A novel regimen with high-dose dual therapy (HDDT) has emerged, but its impact on the gut microbiota is not well understood. This study aimed to evaluate the impact of HDDT on the gut microbiota and compareit with that of bismuth quadruple therapy (BQT). We enrolled outpatients (18-70 years) diagnosed with Helicobacter pylori infection by either histology or a positive 13C-urea breath test (13C-UBT) and randomly assigned to either the BQT or HDDT group. Subjects consented to provide fecal samples which were collected at baseline, Week 2, and Week 14. Amplification of the V1 and V9 regions of the 16S rRNA was conducted followed by high-throughput sequencing. Ultimately, 78 patients (41 patients in the HDDT group and 37 in the BQT group) were enrolled in this study. Eradication therapy significantly altered the diversity of the gut microbiota. However, the alpha diversity rebounded only in the HDDT group at 12 weeks post-eradication. Immediately following eradication, the predominance of Proteobacteria, replacing commensal Firmicutes and Bacteroidetes, did not recover after 12 weeks. Species-level analysis showed that the relative abundances of Klebsiella pneumoniae and Escherichia fergusonii significantly increased in both groups at Week 2. Enterococcus faecium and Enterococcus faecalis significantly increased in the BQT group, with no significant difference observed in the HDDT group. After 12 weeks of treatment, the relative abundance of more species in the HDDT group returned to baseline levels. Eradication of H. pylori can lead to an imbalance in gut microbiota. Compared to BQT, the HDDT is a regimen with milder impact on gut microbiota.

Sources and profiles of toxins in shellfish from the south-central coast of Chile (36°‒ 43° S)

The study of marine toxins in shellfish is of the utmost importance to ensure people's food safety. Marine toxins in shellfish and microalgae in the water column off the south-central coast of Chile (36°‒43° S) were studied in a network of 64 stations over a 14-month period. The relative abundance of harmful species Alexandrium catenella, Alexandrium ostenfeldii, Protoceratium reticulatum, Dinophysis acuminata, Dinophysis acuta, Pseudo-nitzschia seriata group and P. delicatissima group was analyzed. The detection and quantification of lipophilic toxins and domoic acid (DA) in shellfish was determined by UHPLC-MS/MS, and for Paralytic Shellfish Toxins (PSTs) by HPLC-FD with post-column oxidation, while for a culture of A. ostenfeldii a Hylic-UHPLC-MS/MS was used. Results showed that DA, gonyautoxin (GTX)-2, GTX-3 and pectenotoxin (PTX)-2 were detected below the permitted limits, while Gymnodimine (GYM)-A and 13-desmethylespirolide C (SPX-1) were below the limit of quantitation. According to the distribution and abundance record of microalgae, DA would be associated to P. seriata and P. delicatissima-groups, PTX-2 to D. acuminata, and GTX-2, GTX-3, GYM-A, and SPX-1 to A. ostenfeldii. However, the toxin analysis of an A. ostenfeldii culture from the Biobío region only showed the presence of the paralytic toxins C2, GTX-2, GTX-3, GTX-5 and saxitoxin, therefore, the source of production of GYM and SPX is still undetermined.

Community composition of black flies during and after the 2020 vesicular stomatitis virus outbreak in Southern New Mexico, USA

BackgroundVesicular stomatitis virus (VSV), a vector-borne pathogen of livestock, emerges periodically in the western US. In New Mexico (NM), US, most cases occur close to the Rio Grande River, implicating black flies (Simulium spp.) as a possible vector. In 2020, VS cases were reported in NM from April to May, although total black fly abundance remained high until September. We investigated the hypothesis that transience of local VSV transmission results from transient abundance of key, competent black fly species. Additionally, we investigated whether irrigation canals in southern NM support a different community of black flies than the main river. Lastly, to gain insight into the source of local black flies, in 2023 we collected black fly larvae prior to the release of water into the Rio Grande River channel.MethodsWe randomly sub-sampled adult black flies collected along the Rio Grande during and after the 2020 VSV outbreak. We also collected black fly adults along the river in 2021 and 2022 and at southern NM farms and irrigation canals in 2022. Black fly larvae were collected from dams in the area in 2023. All collections were counted, and individual specimens were subjected to molecular barcoding for species identification.ResultsDNA barcoding of adult black flies detected four species in 2020: Simulium meridionale (N = 158), S. mediovittatum (N = 83), S. robynae (N = 26) and S. griseum/notatum (N = 1). Simulium robynae was only detected during the VSV outbreak period, S. meridionale showed higher relative abundance, but lower absolute abundance, during the outbreak than post-outbreak period, and S. mediovittatum was rare during the outbreak period but predominated later in the summer. In 2022, relative abundance of black fly species did not differ significantly between the Rio Grande sites and farm and irrigation canals. Intriguingly, 63 larval black flies comprised 56% Simulium vittatum, 43% S. argus and 1% S. encisoi species that were either extremely rare or not detected in previous adult collections.ConclusionsOur results suggest that S. robynae and S. meridionale could be shaping patterns of VSV transmission in southern NM. Thus, field studies of the source of these species as well as vector competence studies are warranted.Graphical

High immigration rates critical for establishing emigration-driven diversity in microbial communities

Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. Although microbial dispersal constitutes an important ecological process, the effect of dispersal on microbial diversity is poorly understood. Here, we sought to fill this gap by combining a generalized Lotka-Volterra model with experimental investigations. Our model showed that emigration increases the diversity of the community when the immigration rate crosses a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using co-cultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral decreases with the increase of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on the diversity of natural communities.