Shifts In Community Structure Research Articles

Dietary β-hydroxybutyric acid improves the growth performance of young ruminants based on rumen microbiota and volatile fatty acid biosynthesis.

The ketone body β-hydroxybutyric acid (BHB) plays critical roles in cellular proliferation and metabolic fuel utilization; however, its effects on the rumen microbiota remain unknown. Here, three doses of BHB (low, medium, and high) were supplemented to early-weaned goat kids. Compared with controls, the beneficial effects of BHB on growth and rumen development were observed in goats at 90 days of age (d). The low dose of dietary BHB increased the concentration of rumen acetate, propionate, and butyrate on d90. The sequencing results of the rumen microbiota revealed marked shifts in rumen microbial community structure after early-weaned goat kids consumed BHB for 2 months. The signature bacterial ASVs for each treatment were identified and were the main drivers contributing to microbial interactions in the rumen. The bacteria associated with rumen weight were also correlated with body weight. Some classified bacterial signatures, including Prevotella, Olsenella umbonate, and Roseburia faecis, were related to rumen volatile fatty acids and host development. Overall, dietary BHB altered rumen microbiota and environments in young goats, which contributed to rumen development and growth.

Impact of salinity and time on structure and functional potential of wastewater treatment biofilms in intermittent sand bioreactors.

High salt wastewater is produced in industries, including seafood and pickling processing. The salinity in such wastewaters has been shown to negatively impact biological treatment efficacy. Little is known about the changes in the microbial community structure in the mature biological 2 treatment systems, the impacts of salinity on community composition, and the shifts over time during operation. This study aimed to identify the changes in the microbial community due to both salt and days of operation through 16s rRNA sequencing and KEGG functional predictions. Intermittent sand bioreactors (ISBs) with a focus on ammonia treatment were utilized. Results showed that the overall community structure and diversity were distinct as wastewater salinity varied from 0%-1.3%. At 1.3% salinity Zoogloea, a common genus in wastewater treatment plants, was not present and Aequorovita, Thauera and Dokdonella became the dominant genera. Nitrosomonas, an important ammonia oxidizing bacteria, increased in abundance with days of operation but was not significantly impacted by an increase in salinity. This finding was further supported by an increase in predicted nitrification potential with time of operation within all intermittent sand bioreactors tested. These results provide a deeper understanding of the impacts of salinity on microbial community development in biological treatment systems and elucidate the shifts in community structure occurring during early operations and into system maturity.

Functional changes across marine habitats due to ocean acidification.

Global environmental change drives diversity loss and shifts in community structure. A key challenge is to better understand the impacts on ecosystem function and to connect species and trait diversity of assemblages with ecosystem properties that are in turn linked to ecosystem functioning. Here we quantify shifts in species composition and trait diversity associated with ocean acidification (OA) by using field measurements at marine CO2 vent systems spanning four reef habitats across different depths in a temperate coastal ecosystem. We find that both species and trait diversity decreased, and that ecosystem properties (understood as the interplay between species, traits, and ecosystem function) shifted with acidification. Furthermore, shifts in trait categories such as autotrophs, filter feeders, herbivores, and habitat-forming species were habitat-specific, indicating that OA may produce divergent responses across habitats and depths. Combined, these findings reveal the importance of connecting species and trait diversity of marine benthic habitats with key ecosystem properties to anticipate the impacts of global environmental change. Our results also generate new insights on the predicted general and habitat-specific ecological consequences of OA.

Potential influence of bacterial community structure on the distribution of brGDGTs in surface sediments from Yangtze River Estuary to East China Sea

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are special components of bacterial membrane lipids and are ubiquitously found in diverse terrestrial and marine environments. Acidobacteria have been recently evidenced as one of their source microorganisms in terrigenous environments, such as acidic soils and peats. However, the biological sources of brGDGTs, their distributions and ecophysiological responses, and these biotic impacts on the relationships between brGDGT-based proxies and environmental variables (e.g., ambient temperature, pH, and dissolved oxygen content) in the marine realm are poorly understood. In this study, we analyzed C5- and C6-methylated brGDGTs as well as bacterial communities in the surface sediment samples from the Yangtze River Estuary (YRE) to the East China Sea (ECS), aiming to explore the relationship between brGDGT distribution and bacterial composition and to examine how benthic conditions and bacterial communities jointly influence the spatial patterns of brGDGTs from marine sediments. Substantial differences in the spatial distribution of brGDGTs from coast to shelf were observed. The increase in the proportion of brGDGTs with cyclopentyl and C6-methyl moieties (e.g., Ic and IIc’) and #ringstetra values of >0.7 indicate the occurrence of marine-sourced brGDGTs in the shelf. Statistical analyses suggest that the bacterial community structure and the geochemical and environmental variables may contribute 43.56% and 29.97% to the brGDGT distribution, respectively. Multiple significant correlations between bacterial groups at the order level and brGDGT compounds suggest that bacteria such as Gemmatimonadetes, Planctomycetes and Proteobacteria may potentially contribute to the brGDGT production in marine environments. With the consideration of benthic environmental changes, the shift in bacterial community structure could further result in the variations of brGDGT-based proxies incorporating cyclopentyl and C6-methyl moieties that are likely to be produced by benthic marine bacteria. Overall, in addition to environmental conditions of the ocean bottom, the potential influence of bacterial community structure on the distribution of brGDGTs highlights the caution of using brGDGT-based proxies as terrestrial indicators in coastal oceans.

A lag bloom pattern of phytoplankton after freshwater input events revealed by daily samples during summer in Qinhuangdao coastal water, China.

Phytoplankton blooms have become a global concern due to their negative impacts on public health, aquaculture, tourism, and the economic stability of coastal regions. Therefore, elucidating the shifts in phytoplankton community structure and abundance, as well as their environmental drivers, is crucial. However, existing studies often fail to capture the detailed dynamics of phytoplankton blooms and their environmental triggers due to low temporal observation resolution. In this study, high temporal resolution (daily) samples were collected over 43 days to investigate the influence of environmental factors on phytoplankton in Qinhuangdao in the summer. During the observation period, a total of 45 phytoplankton species were identified, comprising 26 Bacillariophyta species, 16 Dinophyta species, 2 Euglenophyta species, and 1 Chromophyta species. Interestingly, a lag bloom pattern of phytoplankton behind freshwater input was observed across day-to-day samples. Phytoplankton blooms typically lagged 1-3 days behind periods of decreased salinity and nutrient input, suggesting that freshwater influx provides the foundational materials and benefits for these blooms. Moreover, the phytoplankton blooms were triggered by six dominant species, i.e., Chaetoceros spp., Pseudo-nitzschia delicatissima, Skeletonema costatum, Protoperdinium spp., Leptocylindrus minimus, Pseudo-nitzschia pungens, and Thalassiosira spp. Consequently, the succession of phytoplankton showed a predominant genera shift in the following sequence: Nitzschia, Protoperdinium, and Prorocentrum - Skeletonema - Pseudo-nitzschia - Gymnodinium - Leptocylindrus. Besides that, a deterministic process dominated phytoplankton community assembly across time series, and DIP is a key factor in shifting the phytoplankton community structures in this area. In summary, our study offers high-resolution observations on the succession of phytoplankton communities and sheds light on the complex and differentiated responses of phytoplankton to environmental factors. These findings enhance our understanding of the dynamics of phytoplankton blooms and their environmental drivers, which is essential for the effective management and mitigation of their adverse impacts.

Enhancing anaerobic digestion performance of oxytetracycline-laden wastewater through micro-nano bubble ozonation pretreatment

This study investigated the potential of micro-nano bubble (MNB) ozonation pretreatment to eliminate oxytetracycline (OTC) from wastewater and improve subsequent anaerobic digestion (AD) performance. The findings revealed that MNB ozonation achieved efficient OTC oxidation (>99 % in 60 min), and significantly enhanced methane production by 51 % compared to conventional ozonation (under 30 min of pretreatment). Additionally, MNB ozonation resulted in a decrease in the soluble chemical oxygen demand and reduced volatile fatty acid accumulation compared to conventional ozonation. Furthermore, the study sheds light on the profound impact of OTC and its oxidation by-products on the sludge microbiome. Exposure to OTC and its oxidation by-products resulted in alterations in extracellular polymeric substances composition and led to significant shifts in microbial community structure. This study highlights the promise of MNB ozonation as an effective approach for pharmaceutical pollutant removal and the optimization of AD performance in wastewater treatment, with implications for improved environmental sustainability.

Grazing-driven shifts in soil bacterial community structure and function in a typical steppe are mediated by additional N inputs

Herbivore grazing and nitrogen (N) fertilization affect soil microbial diversity and community composition both in direct and indirect pathways (e.g., via alterations in soil microenvironment and plant communities); however, their combination effects are still largely unexplored. We carried out a field study to investigate how soil abiotic properties, plant community composition and functional traits altered soil bacterial community structure and function in response to a long-term herbivore grazing (17-year sheep grazing with four stocking rates) and anthropogenic N inputs (6-year N addition with four levels) experiment. We show that a high stocking rate of 8.7 sheep ha−1 (SR8.7) decreased soil bacterial α- and β-diversity, while α- and β-diversity showed hump-shaped and saddle-shaped responses, respectively, with increasing N addition rate, reaching tipping points at the N application rate of 10 g N m−2 year−1 (N10). The synergistic effects of grazing and N addition induced the highest soil bacterial α-diversity at SR2.7 with N10. The contrasting effects of grazing and N addition induced higher soil bacterial β-diversity at SR8.7 with N20. Plant factors (e.g., aboveground biomass of Stipa bungeana and community-weighted mean carbon [CWM_C]), edaphic factors (e.g., soil moisture, pH, NO3−-N, and C:nutrients ratios) and their interactions were the most significant factors affecting the diversity and community composition of bacteria. Our structure equation model (SEM) shows that grazing-induced negative effects on soil pH and plant community composition indirectly increased the β-diversity of soil bacteria, while grazing-induced decreased CWM_C had positive effects on bacterial α-diversity and community structure. However, N addition indirectly increased β-diversity of soil bacteria via changes in soil NO3−-N and plant community composition, while N addition had negative impacts on bacterial α-diversity and community structure via variations in CWM_C. The interaction of grazing and N addition increased the complexity and stability of the bacterial network. Based on the KEGG database, grazing and N addition could accelerate the soil functional potential of C and N cycling. Our findings suggest that N application at a rate of <10 g N m−2 year−1 with a stocking rate of <5.3 sheep ha−1 could maintain the development of soil bacteria in supporting the most important ecosystem functions and services. Complex responses of soil microbes to grazing and N addition indicate the need for deeper investigations of the impacts of global change on microbial involvement in biogeochemical cycles.

Reconnoitre on ichthyofauna of Mahanadi River of India: shifting diversity down the river continuum and linking ecological traits with patterns in biodiversity.

Anthropogenic alterations have paramount impacts on the alpha and beta diversity of aquatic resources, and fishes are predominantly susceptible to such impacts. Mahanadi River, one of the major peninsular rivers of India, has abundant fish resources, which play a significant role in supporting the fishers' livelihoods. The exploratory study in the river conducted for three consecutive years recorded 148 species under 53 families. Cyprinids dominated the fish diversity with 41 species, followed by Bagrids (9) and Sciaenids (7). One hundred-one species under 29 families were reported from the freshwater stretch. With a total of 111 species reported under 48 families, the estuarine and tidal freshwater stretch was more speciose, due to marine migrant species which advent the estuarine and tidal freshwaters stretch for breeding and feeding purposes. Tikarpara, a conserved site within a sanctuary, was the most species-diverse as well as a species-even site. The study also recorded the extension of the distributional range of 3 fish species and also 4 exotic species from the river. The seasonal variations in diversity indicated that the deviations were not prominent in freshwater sites, whereas in tidal brackish water sites, species richness was relatively higher in post-monsoon, and species evenness was higher during monsoon. Taxonomic distinctness test showed that the average taxonomic distinctness was high for tidal estuarine locations as they harbour taxonomically distant fishes. The hierarchical clustering of sites showed the inordinate effect of river gradient and fragmentation on the fish community structure. Analyzing the key drivers of the assemblage structure of the entire river, salinity was the major deterministic factor, and within the freshwater stretch, the major influences were depth, transparency, and specific conductivity. The study concluded that, despite all of its ecological stresses, Mahanadi still supports rich fish diversity, yet there is a notable shift in the fish community structure. There is a need for integrating molecular and morphological tools for the taxonomic revision of many genera and species for proper in situ and ex situ conservation measures and to formulate future biodiversity management plans addressing to reduce the impacts of the ecological threats.

Fungal community structure shifts in litter degradation along forest succession induced by pine wilt disease

Fungi play a crucial role in decomposing litter and facilitating the energy flow between aboveground plants and underground soil in forest ecosystems. However, our understanding how the fungal community involved in litter decomposition responds during forest succession, particularly in disease-driven succession, is still limited. This study investigated the activity of degrading enzyme, fungal community, and predicted function in litter after one year of decomposition in different types of forests during a forest succession gradient from coniferous to deciduous forest, induced by pine wilt disease. The results showed that the weight loss of needles/leaves and twigs did not change along the succession process, but twigs degraded faster than needles/leaves in both pure pine forest and mixed forest. In pure pine forest, peak activities of enzymes involved in carbon degradation (β-cellobiosidase, β-glucosidase, β-D-glucuronidase, β-xylosidase), nitrogen degradation (N-acetyl-glucosamidase), and organic phosphorus degradation (phosphatase) were observed in needles, which subsequently declined. The fungal diversity and evenness (Shannon’s diversity and Shannon's evenness) dropped in twig from coniferous forest to mixed forest during the succession. The dominant phyla in needle/leaf and twig litters were Ascomycota (46.9%) and Basidiomycota (38.9%), with Lambertella pruni and Chalara hughesii identified as the most abundant indicator species. Gymnopus and Desmazierella showed positively correlations with most measured enzyme activities. Functionally, saprotrophs constituted the main trophic mode (47.65%), followed by Pathotroph-Saprotroph-Symbiotroph (30.95%) and Saprotroph-Symbiotroph (10.57%). The fungal community and predicted functional structures in both litter types shifted among different forest types along the succession. These findings indicate that the fungal community in litter decomposition responds differently to disease-induced succession, leading to significant shifts in both the fungal community structure and function.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

ABSTRACT Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Comparative study of high-solid anaerobic digestion at laboratory and industrial scale – Process performance and microbial community structure

High-solid anaerobic digestion (HSD) for biogas production, compared with wet digestion, is attracting interest due to advantages such as reduced fresh water usage, improved digestate quality and potential for high organic loading rates. However, the underlying processes are not well described and evaluated for HSD. In this study, two laboratory-scale reactors (46 L) of plug-flow type were designed to simulate an industrial-scale HSD process co-digesting food waste, agricultural waste and garden residues under thermophilic conditions. Performance of the laboratory-scale HSD process under stable and disturbed conditions was compared with that in industrial-scale reactors. The results showed that the laboratory- and industrial-scale processes had similar efficiency (93 %) and VS-reduction (43 % and 41 %, respectively) and relatively similar specific methane production (339 and 366 NL CH4/kg VS, respectively). Results from tracer studies combined with chemical analyses showed no phase-separation or plug-flow behaviour along the horizontal axis in either laboratory- or industrial-scale reactors, indicating a need for further process optimisation. Analyses of microbial community structure showed high similarity between laboratory- and industrial-scale, but with some differences caused by downscaling. During the experiment, the laboratory- and industrial-scale processes both showed signs of disturbance, i.e. VFA accumulation at NH4+-N levels > 4 g/L, accompanied by a shift in microbial community structure at both scales, with significant increases in relative abundance of e.g. genera Defluviitoga and Methanothermobacter. In conclusion, this study confirmed the validity of simulating HSD at laboratory scale, thus providing valuable insights into biogas production from high-solid substrates, both in laboratory- and industrial-scale processes.

Survivability and proliferation of microorganisms in bentonite with implication to radioactive waste geological disposal: strong effect of temperature and negligible effect of pressure

As bentonite hosts a diverse spectrum of indigenous microorganisms with the potential to influence the long-term stability of deep geological repositories, it is essential to understand the factors influencing microbial activity under repository conditions. Here, we focus on two factors, i.e., temperature and swelling pressure, using a suspension of Cerny Vrch bentonite to boost microbial activity and evaluate microbial response. Suspensions were exposed either to different pressures (10, 12 and 15 MPa; to simulate the effect of swelling pressure) or elevated temperatures (60, 70, 80 and 90 °C; to simulate the effect of cannister heating) for four weeks. Each treatment was followed by a period of anaerobic incubation at atmospheric pressure/laboratory temperature to assess microbial recovery after treatment. Microbial load and community structure were then estimated using molecular-genetic methods, with presence of living cells confirmed through microscopic analysis. Our study demonstrated that discrete application of pressure did not influence on overall microbial activity or proliferation, implying that pressure evolution during bentonite swelling is not the critical factor responsible for microbial suppression in saturated bentonites. However, pressure treatment caused significant shifts in microbial community structure. We also demonstrated that microbial activity decreased with increasing temperature, and that heat treatment strongly influenced bentonite microbial community structure, with several thermophilic taxa identified. A temperature of 90 °C proved to be limiting for microbial activity and proliferation in all bentonite suspensions. Our study emphasizes the crucial role of a deep understanding of microbial activity under repository-relevant conditions in identifying possible strategies to mitigate the microbial potential within the deep geological repository and increase its long-term stability and safety.

Compost application boosts soil restoration in highly disturbed hillslope vineyard

A field trial was carried out to investigate the effects of compost application on a young Cabernet sauvignon vineyard located in a hilly area in the North-East of Italy and subjected to land terracing before plantation. The use of a compost based on manure, pruning residues and pomace at a rate of 65 t ha-1 was compared to the mineral fertilization regime recommended for the vineyards in the area (NPK: 80, 50, 200 kg ha-1). A multi-factorial approach that considered soil chemical properties, microbial community structure and function, vine nutritional and vegetative indexes, yield and quality parameters was applied in the attempt of depict interrelated effects of compost on all these factors. Results of this study show that the application of compost for three consequent years greatly increased soil organic matter content and improved the mineral nutrient availability in the soil. Soil biological fertility showed a slow but significant response to compost addition as from the second year of treatment microbial growth and enzyme activity were increased compared to those of the inorganic fertilization, with special regard to enzymes involved in P cycle. A shift in the soil microbial community structure was also observed in compost-treated soil, with higher presence of copiotrophic bacteria, indicators of soil quality, and phosphorus solubilizing bacteria. A decrease of pathogenic fungal strains was also observed. Organic fertilization increased plant nutrient uptake and vegetative growth compared to those observed in chemically fertilized vines. A trend toward increased yield and improvements for some grape quality parameters such as acidity and pH were observed in the first year of production. These results provide evidence that compost can boost soil fertility restoration in vineyard disturbed by land terracing, allowing for agronomic performances comparable or even improved than those of chemically fertilized vines.

Microbial dynamics in Manaus river, Brazil

Rivers, which are vital ecosystems that support a variety of life forms and provide many ecosystem services, have been degraded by human activities, such as urbanization, pollution, and overexploitation. Habitat restoration projects have been implemented in different parts of the world to restore the ecological health and functioning of degraded rivers. The microbial community that forms biofilms on various substrates is one of the key components of river ecosystems. Organic matter is decomposed and carbon dioxide is produced by these biofilms, which affects the oxygen levels and nutrient cycles in the water. However, the effects of habitat restoration on the biofilm microbial community are not well understood. High-throughput DNA sequencing was used in this study to compare the bacterial composition of biofilms in three types of rivers: degraded urban rivers, urban rivers with restored habitats, and forested rivers that serve as reference conditions. The following questions were aimed to be answered: (i) How is the biofilm bacterial community composition affected by habitat restoration? (ii) How does bacterial diversity change in restored rivers compared to degraded and reference rivers? (iii) What are the environmental factors that influence the biofilm bacterial community composition? It was found that water quality was improved by habitat restoration by increasing the dissolved oxygen and reducing the organic pollutants in urban rivers. A decrease in bacterial diversity and a shift in the biofilm bacterial community structure towards that of the reference forested rivers were accompanied by this. This suggests that the biofilm microbial community can be altered by habitat restoration and its role in processing organic pollutants can be enhanced. However, it was also found that there was still a significant difference in the biofilm bacterial community between the restored and reference rivers, indicating that more time and effort are needed to achieve a similar ecological quality as the natural forested rivers.

Mechanisms of total phosphorus removal and reduction of β-lactam antibiotic resistance genes by exogenous fungal combination activated sludge

This study utilized Trichoderma and activated sludge to construct combined activated sludge (TAS). The metagenomic approach was employed to examine the shifts in microbial community structure and function of TAS under amoxicillin stress and investigate the mechanism underlying the reduction of β-lactam antibiotic resistance genes (β-ARGs). The findings demonstrated that the elevated aundance of glpa, glpd, ugpq, glpq, and glpb were primarily responsible for the reduction in total phosphorus (TP) removal by TAS. The increased abundance of Proteobacteria and Verrucomicrobia led to enhanced expression of ugpb, phnd, and phne, thereby improving the TP removal of TAS. Furthermore, antibiotic inactivation has gradually become the primary antibiotic resistance mechanism in TAS. Specifically, an increase in the abundance of OXA-309 in TAS will decrease the probability of amoxicillin accumulation in TAS. A decrease in β-ARGs diversity confirmed this. This study presents a novel approach to reducing antibiotic and ARG accumulation in sludge.

Effect of HRT on nitrogen removal from low carbon source wastewater enhanced by slurry and its mechanism

Insufficient carbon sources in low-carbon wastewater have consistently hindered nitrogen removal performance. This work utilized slurry after anaerobic digestion as an additional carbon source, and the optimal hydraulic retention time (HRT) parameters were obtained through adjustment. The findings revealed that, under HRT conditions of 24–12 h, the discharge standards of wastewater treatment plants (WWTPs) could be met. It had been proven that HRT 12 h was the more cost-effective parameter for application in WWTPs, and the removal efficiencies for COD, NH4+-N, NO3–-N, and TN reached impressive levels of 82.43%, 95.24%, 77.49%, and 86.70%, respectively. However, the HRT 6 h struggled to achieve efficient wastewater treatment. Mechanistic analysis demonstrated that shortening the HRT resulted in considerably higher microbial richness, diversity, and evenness, causing notable shifts in microbial community structure. Additionally, a shortened HRT reduced the enrichment abundance of key bacterial phyla (Proteobacteria, Bacteroidetes) and genera (Hydrogenophaga, Filimonas, Meganema) that played an important role in nitrogen and organic matter removal. Furthermore, a shortened HRT increased hydraulic shear forces, impeding the enrichment of carbon and nitrogen metabolism pathways, and reducing the abundance of essential genes associated with glycolysis (HK, pfkA, FBA, GAPDH) and nitrogen metabolism processes (narG, narH, narI, norB, nirS, nosZ). It was noteworthy that the microbial community under the HRT 6 h condition carried the highest risk of microbial pathogenicity. This work revealed the optimal parameters, and carbon and nitrogen metabolism mechanism of wastewater treatment systems with slurry as a carbon source for the first time, and provided novel ideas and insights for low-carbon wastewater treatment.

Tissue-specific transcriptional response of post-larval clownfish to ocean warming

Anthropogenically driven climate change is predicted to increase average sea surface temperatures, as well as the frequency and intensity of marine heatwaves in the future. This increasing temperature is predicted to have a range of negative physiological impacts on multiple life-stages of coral reef fish. Nevertheless, studies of early-life stages remain limited, and tissue-specific transcriptomic studies of post-larval coral reef fish are yet to be conducted. Here, in an aquaria-based study we investigate the tissue-specific (brain, liver, muscle, and digestive tract) transcriptomic response of post-larval (20 dph) Amphiprion ocellaris to temperatures associated with future climate change (+3 °C). Additionally, we utilized metatranscriptomic sequencing to investigate how the microbiome of the digestive tract changes at +3 °C. Our results show that the transcriptional response to elevated temperatures is highly tissue-specific, as the number of differentially expressed genes (DEGs) and gene functions varied amongst the brain (102), liver (1785), digestive tract (380), and muscle (447). All tissues displayed DEGs associated with thermal stress, as 23 heat-shock protein genes were upregulated in all tissues. Our results indicate that post-larval clownfish may experience liver fibrosis-like symptoms at +3 °C as genes associated with extracellular matrix structure, oxidative stress, inflammation, glucose transport, and metabolism were all upregulated. We also observe a shift in the digestive tract microbiome community structure, as Vibrio sp. replace Escherichia coli as the dominant bacteria. This shift is coupled with the dysregulation of various genes involved in immune response in the digestive tract. Overall, this study highlights post-larval clownfish will display tissue-specific transcriptomic responses to future increases in temperature, with many potentially harmful pathways activated at +3 °C.

Unlocking the microbial diversity and the chemical changes throughout the fermentation process of “hákarl”, Greenland shark

Hákarl is a unique traditional Icelandic product and is obtained by fermenting and drying Greenland shark (Somniosus microcephalus). However, little is known about the chemical and microbial changes occurring during the process. In this small-scale industrial study, fresh and frozen shark meat was fermented for eight and seven weeks, respectively, and then dried for five weeks. During the fermentation, trimethylamine N-oxide levels decreased to below the limit of detection within five weeks and pH increased from about 6 to 9. Simultaneously, trimethylamine and dimethylamine levels increased significantly. Total viable plate counts, and specific spoilage organisms increased during the first weeks of the fermentation period but decreased during drying. Culture-independent analyses (16S rRNA) revealed gradual shifts in the bacterial community structure as fermentation progressed, dividing the fermentation process into three distinct phases but stayed rather similar throughout the drying process. During the first three weeks of fermentation, Photobacterium was dominant in the fresh group, compared to Pseudoalteromonas in the frozen group. However, as the fermentation progressed, the groups became more alike with Atopostipes, Pseudomonas and Tissierella being dominant. The PCA analysis done on the chemical variables and 16S rRNA analysis variables confirmed the correlation between high concentrations of TMAO and Pseudoalteromonas, and Photobacterium at the initial fermentation phase. During the final fermentation phase, correlation was detected between high concentrations of TMA/DMA and Atopostipes, Pseudomonas and Tissierella. The results indicate the possibility to shortening the fermentation period and it is suggested that the microbial community can potentially be standardized with starter cultures to gain an optimal fermentation procedure.

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing.

Assembling a functional consortium and identifying novel degraders from contaminated environments are still challenging due to the large diversity of microorganisms and the difficulty in isolating pure cultures. Here, we constructed a relatively simple functional consortium by enriching 1,4-dioxane-degrading-consortia using a culture-dependent dilution-to-extinction (DTE) method and reported a new key dioxane-degrader Shinella sp. Our results showed that serial dilution and reculture led to a divergence in the degradation ability of each consortium. Next-generation sequencing data revealed that the divergence in degradation performance was due to the reassembly of microbiota in the DTE process, which occurred most notably in 10-8 and 10-9 dilutions. The shift in community structure at 10-9 prevented the recovery of 1,4-dioxane degradation capacity, and the newly dominant taxa, Xanthobacter and Acinetobacter, struggled to replace the original dominant genus Shinella for 1,4-dioxane biodegradation. Combining differential analysis of community structure and metabolic function, we confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, we verified our findings using our isolated dioxane-degrading bacteria, Shinella yambaruensis, resulting in the rapid recovery of degradation performance of a 10-9 dilution consortium with Xanthobacter and Acinetobacter as the dominant microbiota. Taken together, this study provides a strategy for self-assembling functional consortiums and identifying the key degraders to explore the underlying biological mechanisms of enriched contaminant-degrading consortia.IMPORTANCEAssembling a functional microbial consortium and identifying key degraders involved in the degradation of 1,4-dioxane are crucial for the design of synergistic consortia used in enhancing the bioremediation of 1,4-dioxane-contaminated sites. However, due to the vast diversity of microbes, assembling a functional consortium and identifying novel degraders through a simple method remain a challenge. In this study, we reassembled 1,4-dioxane-degrading microbial consortia using a simple and easy-to-operate method by combining dilution-to-extinction and reculture techniques. We combined differential analysis of community structure and metabolic function and confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, a new dioxane-degrading bacterium was isolated, Shinella yambaruensis, which verified our findings. These results demonstrate that DTE and reculture techniques can be used beyond diversity reduction to assemble functional microbial communities, particularly to identify key degraders in contaminant-degrading consortia.

Invasion of Bythotrephes longimanus and Cercopagis pengoi in Lake Champlain: Impacts on the Native Zooplankton Community

The zooplankton community of Lake Champlain has been altered over the past decade due to the introduction of two predatory zooplankton species. Bythotrephes longimanus Leydig, 1860 was first detected in Lake Champlain in August 2014, and Cercopagis pengoi (Ostroumov, 1891) was detected in August 2018. Monitoring for both invasive species at 15 lake sites using whole water tow sampling has been ongoing since 2010 with no detection of either species until 2014. Utilizing data from the Lake Champlain long-term monitoring program, we assessed pre- and post-invasion population dynamics of both invasive species on the native zooplankton community. Our results showed shifts in community structure following invasion, including a reduction in Diacyclops thomasi (Forbes, 1882) populations by both invaders and a reduction in Daphnia retrocurva Forbes, 1882 following the introduction of B. longimanus. Other cyclopoids, bosminids, and rotifers were also reduced, corresponding to both introduced species. The native large-bodied plankton predator Leptodora kindtii (Focke, 1844) appears to be unable to coexist with either invasive predatory cladoceran, displaying seasonal partitioning between L. kindtii and the Cercopagidae. These findings suggest that the invasion of both large predators in Lake Champlain have impacted pelagic zooplankton community structure.