Taxonomic Community Composition Research Articles

Taxonomic diversity of extremophilic prokaryotes adapted to special environmental parameters in Hungary: a review.

The taxonomic and metabolic diversity of prokaryotes and their adaptability to extreme environmental parameters have allowed extremophiles to find their optimal living conditions under extreme conditions for one or more environmental parameters. Natural habitats abundant in extremophilic microorganisms are relatively rare in Hungary. Nevertheless, alkaliphiles and halophiles can flourish in shallow alkaline lakes (soda pans) and saline (solonetz) soils, where extreme weather conditions favor the development of unique bacterial communities. In addition, the hot springs and thermal wells that supply spas and thermal baths and provide water for energy use are suitable colonization sites for thermophiles and hyperthermophiles. Polyextremophiles, adapted to multiple extreme circumstances, can be found in the aphotic, nutrient-poor and radioactive hypogenic caves of the Buda Thermal Karst, among others. The present article reviews the organization, taxonomic composition, and potential role of different extremophilic bacterial communities in local biogeochemical cycles, based on the most recent studies on extremophiles in Hungary.

Anthropogenic Eutrophication Drives Major Food Web Changes in Mwanza Gulf, Lake Victoria

AbstractDiscerning ecosystem change and food web dynamics underlying anthropogenic eutrophication and the introduction of non-native species is necessary for ensuring the long-term sustainability of fisheries and lake biodiversity. Previous studies of eutrophication in Lake Victoria, eastern Africa, have focused on the loss of endemic fish biodiversity over the past several decades, but changes in the plankton communities over this same time remain unclear. To fill this gap, we examined sediment cores from a eutrophic embayment, Mwanza Gulf, to determine the timing and magnitude of changes in the phytoplankton and zooplankton assemblages over the past century. Biogeochemical proxies indicate nutrient enrichment began around ~ 1920 CE and led to rapid increases in primary production, and our analysis of photosynthetic pigments revealed three zones: pre-eutrophication (prior to 1920 CE), onset of eutrophication with increases in all pigments (1920–1990 CE), and sustained eutrophication with cyanobacterial dominance (1990 CE–present). Cladoceran remains indicate an abrupt decline in biomass in ~ 1960 CE, in response to the cumulative effects of eutrophication and lake-level rise, preceding the collapse of haplochromine cichlids in the 1980s. Alona and Chydorus, typically benthic littoral taxa, have remained at relatively low abundances since the 1960s, whereas the abundance of Bosmina, typically a planktonic taxon, increased in the 1990s concurrently with the biomass recovery of haplochromine cichlid fishes. Overall, our results demonstrate substantial changes over the past century in the biomass structure and taxonomic composition of Mwanza Gulf phytoplankton and zooplankton communities, providing a historical food web perspective that can help understand the recent changes and inform future resource management decisions in the Lake Victoria ecosystem.

Effect of Mineral Fertilizers and Pesticides Application on Bacterial Community and Antibiotic-Resistance Genes Distribution in Agricultural Soils

Soils are a hotspot for the emergence and spread of antibiotic resistance. The effects of agrochemical treatments on the bacterial community of agricultural soils and the content of antibiotic-resistance genes (ARGs) were studied. Treatments included the following: control, mineral fertilizers (NPKs), pesticides, and the combined treatment of soils under soya (Glycine max), sunflower (Helianthus annuus L.), and wheat (Triticum aestivum). Bacterial community taxonomic composition was studied using 16S rRNA gene sequencing. The content of 10 ARGs and 3 integron genes (intI1, intI2, intI3) was determined using quantitative real-time PCR. The results showed that the treatments had little effect on the taxonomic composition and diversity of the soil bacterial community. The most significant factors determining differences in the microbial community were sampling time and soil physico-chemical parameters. A significant role of the bacterial community in ARG distribution in soils was demonstrated. Representatives of the Pseudomonas, Bacillus, Sphingomonas, Arthrobacter genera, and the Nocardioidaceae and Micrococcaceae families were likely ARG hosts. The presence of integron genes of all three classes was detected, the most numerous being intI3. This work provides important information on the role of agricultural soils in ARG transfer, and the findings may be useful for sustainable and safe agricultural development.

Testing a Hyperspectral, Bio‐Optical Approach to Identification of Phytoplankton Community Composition in the Chesapeake Bay Estuary

AbstractThe multi‐to hyperspectral evolution of satellite ocean color sensors is anticipated to enable satellite‐based identification of phytoplankton biodiversity, a key factor in aquatic ecosystem functioning and upper ocean biogeochemistry. In this work the bio‐optical Phytoplankton Detection with Optics (PHYDOTax) approach for deriving taxonomic (class‐level) phytoplankton community composition (PCC, e.g. diatoms, dinoflagellates) from hyperspectral information is evaluated in the Chesapeake Bay estuary on the U.S. East Coast. PHYDOTax is among relatively few optical‐based PCC differentiation approaches available for optically complex waters, but it has not yet been evaluated beyond the California coastal regime where it was developed. Study goals include: (a) testing the approach in a turbid estuary including novel incorporation of colored dissolved organic matter (CDOM) and non‐algal particles (NAP), and (b) performance assessment with both synthetic mixture and field data sets. Algorithm skill was robust on synthetic mixtures. Using field data, cryptophyte and/or cyanophyte phytoplankton groups were predicted, but diatom and dinoflagellate detection was not conclusive. For one field data set, small but significant improvements were observed in predicted PCC groups when tested with incorporation of CDOM and NAP into the algorithm, but not for the second field data set. Sensitivity to three hyperspectral‐relevant spectral resolutions (1, 5, 10 nm) was low for all field and synthetic data. PHYDOTax can identify some phytoplankton groups in the estuary using hyperspectral, field‐collected measurements, but validation‐quality data with broad temporospatial coverage are needed to determine whether the approach is robust enough for science applications.

Decomposing benefits: Examining the impact of beech deadwood on soil properties and microbial diversity

Deadwood is an important element of forest ecosystems that affects many of its components, including the soil environment. Our research is an attempt to determine the role of decaying wood in shaping the properties of forest soils in mountain ecosystems. The aim of our research was to present the influence of beech deadwood on physicochemical properties and microbiological diversity of soils. The research was carried out in the Baba Góra Massif at its northern exposure. The research plots were established in the altitude gradient at 600, 800 and 1000 m above sea level. On each plot, samples were taken from decaying wood, from the soil directly under the decaying log, and a soil sample 1 m from the log as a control. We determined the basic properties of the samples, that is pH, C and N concentration and lignin content. The enzymatic activity and additionally, the taxonomic composition of soil bacterial and fungal communities was determined in the collected samples. Our research indicates the important role of decaying beech wood in shaping the properties of forest soils. We noted a positive effect of decaying wood on the properties of the tested soils. Soils affected by deadwood were characterized by significantly higher pH, C and N concentrations compared to control soils, regardless of their location in the altitude gradient. Additionally, we found that soils affected by decaying wood are characterized by a different composition of microorganisms regardless of their location in the altitude gradient. In control soil the fungal and bacterial alpha diversity were lowest compared with the deadwood and soil under the influence of deadwood. Our results may have practical applications in the management of forest ecosystems. The presented results indicate the possibility of leaving deadwood in order to improve its basic physicochemical properties and increase microbial diversity.

Peri-urban Mediterranean plant communities are shaped by chronic anthropogenic disturbances

Peri-urban plant communities perform key ecological functions. However, the integrity of peri-urban vegetation is threatened by the continuous expansion of built-up areas and anthropogenic activities, which result in low-intensity, but continuous and pervasive chronic anthropogenic disturbances (CADs). Despite the growing attention to the ecological role of peri-urban vegetation patches, the assessment of the relationship between CADs and typical Mediterranean plant communities at the local scale is still lacking. In this work, both the compositional and functional responses to typical CADs of five vegetation types were assessed in 48 plots, located around the city of Genoa (Italy). The main anthropogenic and environmental drivers of species composition were identified through a Non-Metric Multidimensional Scaling, and selected variables were used to fit a partial Redundancy Analysis. Differences in the number of alien species in relation to total CAD intensity were assessed with a Kruskal-Wallis test. Regarding functional composition, the community weighted mean values (CWMs) of five functional traits were computed for each plot. Generalized linear models were then fitted to assess the relationship between the CWMs and CADs intensity. Our results showed that the specific composition of peri-urban plant communities of Genoa is shaped by interacting environmental and anthropogenic factors. Considering composition, CADs promote the increase of alien species’ number. Moreover, the increased intensity of CADs altered the functional composition, with increasing specific leaf area, leaf nitrogen content and seed bank longevity. Overall, the effect of typical Mediterranean CADs is more pronounced on the functional composition than on the taxonomic composition of peri-urban plant communities. This work highlights the relevance at the local scale of the typical CADs of the Mediterranean area in influencing the different vegetation types that characterise a peri-urban zone.

Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis.

Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS. To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites. A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored. In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.

Effect of Simulated Eutrophication of Peatlands on the Microbiome of Utricularia vulgaris L.

Global climate change and increasing human impact are the main factors intensifying eutrophication of peatland ecosystems. Due to the high sensitivity of certain groups of microorganisms, they can serve as indicators of the degree of eutrophication and thereby provide much important information for assessment of the state of peatland ecosystems. However, there is still little knowledge of how changes in the fertility of the environment can affect the microbiome of carnivorous plants in these ecosystems. This study was conducted to verify the following hypotheses: (1) the microbiome of carnivorous plant traps reflects the trophic status of the habitat; (2) an increase in the concentration of biogenic compounds causes a greater increase in the size of microbial communities in the aquatic environment than in the traps. An experiment was carried out in laboratory conditions to determine the effect of simulated eutrophication on the microbiome of Utricularia vulgaris L. An experimental increase in habitat fertility caused an increase in the abundance of bacteria, flagellates, testate amoebae, ciliates, and rotifers, while a decrease in abundance was observed for crustaceans. The increase in the concentration of biogenic compounds also modified the taxonomic composition of communities of microorganisms and small metazoa as well as the strength of trophic relationships; as the trophic level increased, the relationships between bacteria and heterotrophic flagellates; bacteria and testate amoebae; and bacteria and ciliates became stronger.

Long-term restoration with organic amendments is clearer evidenced by soil organic matter composition than by changes in microbial taxonomy and functionality

Here, a degraded soil, located in a semi-arid Mediterranean region, was characterized 17 years after organic amendment with sludge or compost (differing in their stabilization degree) for restoration purposes. To do this, (i) soil physicochemical properties and plant cover, (ii) soil organic matter (SOM) content and composition, (iii) soil basal respiration and enzymatic activities, and (iv) abundance, taxonomic composition, and functionality (shotgun metagenomics) of microbial communities were studied. Increased SOM and nutrient contents were found in soil from amended plots with respect to the control, with no differences between amendment types. This is explained by the lasting effects of organic amendments and the higher plant cover. Thermal and pyrolytic analyses showed that the restoration process enriched soil mainly with SOM of intermediate recalcitrance and of high chemical diversity. SOM composition did not differ between amendment types. Increased microbial abundances and activities were found in the amended plots, without differences between compost and sludge. Shotgun metagenomics showed that microbial communities changed in taxonomic and functional terms between amended and unamended plots, but these differences were rather limited. The taxonomic differences between treatments were mainly driven by increasing abundances of Actinobacteria and decreasing abundances of Proteobacteria in soil from amended plots. Soil microbial communities in amended plots showed some functional adaptation to the increased nutrient contents and predominant nutrients forms. This, together with the higher microbial abundances detected, explained the conspicuous soil enzymatic activities reported in amended plots. The effectiveness of the studied soil restoration process was confirmed here from an integrative perspective.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by ‘Candidatus Phytoplasma pini’ as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, ‘Ca. Phytoplasma pini’ is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

A Comparative Investigation of the Bile Microbiome in Patients with Choledocholithiasis and Cholecystolithiasis through Metagenomic Analysis.

While the precise triggers of gallstone formation remain incompletely understood, it is believed to arise from a complex interplay of genetic and environmental factors. The bile microbiome is being increasingly recognized as a possible contributor to the onset of gallstone disease. The primary objective of this study was to investigate distinctions in the microbial communities within bile specimens from patients with choledocholithiasis (common bile duct stones) and cholecystolithiasis (gallbladder stones). We employed massively parallel sequencing of the 16S rRNA gene to examine the microbial communities within bile samples obtained from 28 patients with choledocholithiasis (group DS) and cholecystolithiasis (group GS). The taxonomic composition of the bile microbial communities displayed significant disparities between the group DS and the group GS. Within the 16 prevalent genera, only Streptococcus, Ralstonia, Lactobacillus, and Enterococcus were predominantly found in the group GS. In contrast, the group DS displayed a more diverse range of genera. The alpha diversity of bile specimens was also notably lower in the group GS compared to the group DS (p = 0.041). Principal coordinate analysis unveiled distinct clustering of bile microbial communities depending on the location of the gallstone. Linear discriminant analysis effect size analysis, with a score threshold of >3 and the Kruskall-Wallis test (α < 0.05), recognized Bacilli and Lactobacillales as potential taxonomic markers for distinguishing patients with cholecystolithiasis limited to the gallbladder. Significant variations were found in the distribution and diversity of bile microbial communities between patients with choledocholithiasis and cholecystolithiasis. This observation suggests that alterations in the bile microbiome may contribute to the development of gallstones in these patients.

Beneficial effects of native broadleaved forests on canopy beetle diversity are not reduced by admixture of non‐native conifers

Abstract Biodiversity loss and vast forest diebacks due to climate change‐induced disturbances require adapted forest management strategies that reconcile economic interests and conservation. Tree species selection, including admixture of fast‐growing and drought‐tolerant non‐native species to native forests, is an increasingly considered approach. However, we lack data on how such mixtures affect native forest biodiversity, especially for the sparsely researched major above‐ground part of trees, the canopy. In 40 temperate forest plots in northwest Germany, we investigated how monocultures and admixtures of introduced fast‐growing conifers (native Norway spruce planted outside its natural range and non‐native Douglas fir) to native broadleaved European beech forests affect abundance, biomass, taxonomic and functional diversity and community composition of canopy beetles across trophic guilds. Diverse arthropod communities are vital contributors to forest health and resilience, and therefore valuable indicators to assess and evaluate forestry measures. Monospecific stands of non‐native Douglas fir reduced canopy beetle abundance and diversity compared to native European beech, exceeding the negative effects of Norway spruce. These effects were more pronounced for herbivorous beetles, while they were less strong for predators. Beetle communities in monospecific Norway spruce stands had low functional richness. European beech and mixtures with non‐native Douglas fir had high dissimilarity between local communities (turnover, i.e. beta diversity) and high total beetle diversity at landscape scale (gamma diversity). Mixtures generally mitigated the negative effects of introduced conifers, including shifts in species community composition compared to native European beech. Synthesis and applications: Monospecific stands of fast‐growing non‐native Douglas fir and native Norway spruce planted outside its natural occurrence showed undesirable effects such as low diversity and a shifted community composition of canopy beetles compared to native European beech. However, mixed stands mitigated negative effects and specifically admixed non‐native Douglas fir did not reduce species turnover and landscape‐scale beetle diversity. In line with recent studies on other forest taxa, we conclude that admixtures of introduced conifers to European beech forests, but not monospecific plantations, can potentially serve as a compromise between conservational and economic interests.

Changes in taxonomic and functional composition of subalpine plant communities in response to climate change under contrasting conditions of bedrock and snow cover duration

AbstractQuestionsWe assessed interactions between climate change, bedrock types and snow cover duration on the trajectories of taxonomic and functional composition of subalpine plant communities. We predict (i) an increase in species richness on siliceous bedrock due to a reduced competition and a decrease in richness on calcareous bedrock due to increasing drought stress; (ii) decreasing snow cover duration should induce a higher shrub encroachment in hollows as compared to ridges; and (iii) increasing growing season temperature should induce taller sizes and more conservative growth traits, in particular in hollows.LocationSubalpine belt of the Grandes Rousses mountain range, southwestern Alps (France).Methods189 vegetation plots were sampled in 1997 and 2017–2018. The duration of snow cover was assessed during two years in 1995–1997 and five functional traits were measured on 108 species in 2021. We performed multivariate analyses, quantified community‐weighted means (CWM) of traits and used ANOVAs to detect responses to local‐scale factors and changes in snow cover, temperature and precipitation since 1997 according to a nearby meteorological station.ResultsOverall, taxonomic composition weakly changed and changes were more dependent on the position of communities along the snow cover duration gradient than on their bedrock type. The abundance of drought‐tolerant species increased at the border of hollows and there was, over all communities, a slight increase in the abundance of dwarf shrubs and tall herbaceous species, a strong decrease in short herbaceous species and, thus, an overall decrease in species richness. There were important overall changes in CWM of size traits, in particular leaf area which increased the most in hollows irrespective of bedrock types.ConclusionIn this subalpine site the effects of decreasing snow cover duration overwhelmed the effects of bedrocks, which may explain the overall increase in competitive species and decrease in species richness.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1–3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.

Soil Microbiome of Abandoned Plaggic Podzol of Different-Aged Fallow Lands and Native Podzol in South Taiga (Leningrad Region)

The soil microbiome is composed of various communities that play an important role in the existence of ecosystem services and the sustainable functioning of ecosystems under high anthropogenic loads. The transition of soils to a fallow state and their subsequent transformation lead to a notable alteration in the taxonomic composition of the soil microbiome, impacting the biochemical processes within the soil and its fertility levels. The object of this study comprised different-aged fallow soils of the southern taiga in the vicinity of Ban’kovo village, Leningrad region. The method comprising the high-throughput sequencing of 16S rRNA gene fragments using an Illumina MiSEQ sequencer was used to analyze the microbial community. The general processing of sequences was carried out with the dada2 (v1.14.1) package. It was found that the morphological organization of fallow soils has significant differences from the native podzol. In fallow soils, there are signs of leaching expressed in the accumulation of leached mineral particles, which indicates the degradation of the fallow–arable horizon. At the same time, there is a decrease in the content of P2O5 and K2O and an increase in the content of N-NH4 and N-NO3 in fallow soil. The analysis of alpha diversity index values showed that the highest level of alpha diversity in the microbial community is characteristic of 40-year-old soil, the alpha diversity index decreased with the increasing time of the fallow state, and the lowest alpha diversity index was observed in the native podzol. According to the values of the beta diversity index, a high correlation between the soil microbiome and the physicochemical characteristics of the soil was revealed, which indicates the formation of functional specialization in the studied microbial communities. As a result of the study of the taxonomic composition of microbial communities in fallow soils, it was found that the most represented microbial communities in fallow soils belong to Nitrosomonadaceae (Pseudomonadota), Mycobacterium (Actinobacteria), Nitrospira (Nitrospirota), and Luteolibacter (Verrucomicrobiota). The duration of post-agrogenic transformation is the leading factor influencing the changes in microbial communities; so, with an increase in the time that soils were in a fallow state, an increase in the oligotrophic microbial community was observed.

Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil

The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.

Parasites alter food-web topology of a subarctic lake food web and its pelagic and benthic compartments

We compared three sets of highly resolved food webs with and without parasites for a subarctic lake system corresponding to its pelagic and benthic compartments and the whole-lake food web. Key topological food-web metrics were calculated for each set of compartments to explore the role parasites play in food-web topology in these highly contrasting webs. After controlling for effects from differences in web size, we observed similar responses to the addition of parasites in both the pelagic and benthic compartments demonstrated by increases in trophic levels, linkage density, connectance, generality, and vulnerability despite the contrasting composition of free-living and parasitic species between the two compartments. Similar effects on food-web topology can be expected with the inclusion of parasites, regardless of the physical characteristics and taxonomic community compositions of contrasting environments. Additionally, similar increases in key topological metrics were found in the whole-lake food web that combines the pelagic and benthic webs, effects that are comparable to parasite food-web analyses from other systems. These changes in topological metrics are a result of the unique properties of parasites as infectious agents and the links they participate in. Trematodes were key contributors to these results, as these parasites have distinct characteristics in aquatic systems that introduce new link types and increase the food web’s generality and vulnerability disproportionate to other parasites. Our analysis highlights the importance of incorporating parasites, especially trophically transmitted parasites, into food webs as they significantly alter key topological metrics and are thus essential for understanding an ecosystem’s structure and functioning.

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.

Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.

Declining salinity and increasing temperature reduce the diversity and resilience of benthic diatoms.

Climate change will modify the marine ecosystem in several ways, but the effects of changing climate on benthic diatoms, which are one of the most important photosynthesizing organism groups in benthic habitats, are poorly studied. We conducted a mesocosm experiment to investigate the effects of increasing temperature and decreasing salinity on the taxonomic and functional diversity of benthic diatoms. We showed that decreasing salinity affects the taxonomic and functional composition of communities, and the threshold salinity for community composition is ~5. This indicates that when climate change leads to decreasing salinity in brackish systems, the most pronounced changes in communities occur in areas where salinity decreases from >5 to <5. We also showed that both increasing temperature and decreasing salinity exert stress on communities and, hence, lead to the decrease of the alpha and beta diversity of communities. This indicates that climate change reduces the size of the species pool of diatoms. Our results show that, along with the changing climate, we can expect benthic diatom communities to become less diverse and less resilient.

Effects of the Abandonment of Traditional Cultural Practices on Epiphytic Bryolichenic Communities in Chestnut Orchards in North-West Spain

This study delves into the impact of contrasting management practices on epiphytic bryolichenic communities, shedding light on their divergent responses to management regimes on Castanea sativa Mill. orchards. Lichens and bryophytes were sampled in managed and abandoned plots, in 95 trees, in north and south sides and at two heights in Galicia (NW Spain). The studied groups exhibited opposing reactions to these management practices; bryophytes suffered adverse effects in managed stands, experiencing reduced cover and species richness compared to abandoned orchards, while lichens displayed heightened cover and species diversity. The size of trees, included as a covariate in our analyses, displayed no significant impact on the overall species richness of lichens or bryophytes, although it did influence the cover of specific functional traits. These differing outcomes may be linked to alterations in environmental conditions brought by management interventions. Furthermore, the study uncovered divergent responses within the taxonomic and functional composition of epiphytic communities. Different species and functional groups exhibited varying reactions to changing environmental conditions, making predictions a complex endeavour. In conclusion, this research emphasizes the need for management strategies that account for the diverse ecological requirements of different species and functional groups since no single management regime will suit all species or functional groups.