Enhancing Human Health and Wellbeing through Sustainably and Equitably Unlocking a Healthy Ocean's Potential.

A healthy ocean is essential for human health, and yet the links between the ocean and human health are often overlooked. By providing new medicines, technologies, energy, foods, recreation, and inspiration, the ocean has the potential to enhance human health and wellbeing. However, climate change, pollution, biodiversity loss, and inequity threaten both ocean and human health. Sustainable realisation of the ocean's health benefits will require overcoming these challenges through equitable partnerships, enforcement of laws and treaties, robust monitoring, and use of metrics that assess both the ocean's natural capital and human wellbeing. Achieving this will require an explicit focus on human rights, equity, sustainability, and social justice. In addition to highlighting the potential unique role of the healthcare sector, we offer science-based recommendations to protect both ocean health and human health, and we highlight the unique potential of the healthcare sector tolead this effort.

Bee monitoring by community scientists: comparing a collections-based program with iNaturalist.

Bee monitoring, or widespread efforts to document bee community biodiversity, can involve data collection using lethal (specimen collections) or non-lethal methods (observations, photographs). Additionally, data can be collected by professional scientists or by volunteer participants from the general public. Collection-based methods presumably produce more reliable data with fewer biases against certain taxa, while photography-based approaches, such as data collected from public natural history platforms like iNaturalist, can involve more people and cover a broader geographic area. Few efforts have been made to quantify the pros and cons of these different approaches. We established a community science monitoring program to assess bee biodiversity across the state of Pennsylvania (USA) using specimen collections with nets, blue vane traps, and bowl traps. We recruited 26 participants, mostly Master Gardeners, from across the state to sample bees after receiving extensive training on bee monitoring topics and methods. The specimens they collected were identified to species, stored in museum collections, and the data added to public databases. Then, we compared the results from our collections to research-grade observations from iNaturalist during the same time period (2021 and 2022). At state and county levels, we found collections data documented over twice as much biodiversity and novel baseline natural history data (state and county records) than data from iNaturalist. iNaturalist data showed strong biases toward large-bodied and non-native species. This study demonstrates the value of highly trained community scientists for collections-based research that aims to document patterns of bee biodiversity over space and time.

A phylogenetic study of Micareamelaeniza and similar-looking species (Pilocarpaceae) unveils hidden diversity and clarifies species boundaries and reproduction modes.

Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micareamelaeniza group focussing on M.melaeniza, M.nigella and M.osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micareaeurasiatica Kantelinen & G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M.osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.

Forecasting potential invaders to prevent future biological invasions worldwide.

The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.

[Protecting biodiversity and sustainable sciences]. / Protection de la biodiversité et sciences durables.

The latest IPBES report clearly showed that pollution and proliferation of invasive alien species constituted two of the five major factors responsible for the biodiversity decline. Faced with this situation, we present here the development of nature-based solutions in response to these two challenges. This approach has firstly made it possible to progress in understanding the adaptation strategies of plants and associated micro-organisms to respond to attacks such as pollution. Thus, relevant studies showed that certain plant species are able to grow in environments contaminated with metallic elements, or even to sequester toxic pollutants in their leaves or their roots. This research has made it possible to provide original solutions for the ecological restoration of soils and the decontamination of aquatic systems using dead invasive exotic plant species. The promotion of these solutions through the concept of ecocatalysis, at the interface of ecology and chemistry, contributed to make them sustainable and economically viable.

Title: Protection de la biodiversité et sciences durables. Abstract: Le dernier rapport de l'IPBES a clairement montré que la pollution et la multiplication des espèces exotiques envahissantes constituaient deux des cinq facteurs majeurs responsables du déclin de la biodiversité. Face à cette situation, nous présentons dans cette brève revue le développement de solutions fondées sur la nature pour répondre à ces deux défis. Cette approche a tout d'abord permis de progresser dans la compréhension des stratégies d'adaptation des plantes et des microorganismes associés, pour répondre à des agressions telles que celle de la pollution. Ainsi, il a pu être démontré que certaines espèces végétales sont capables de se développer dans des milieux contaminés par des éléments métalliques, voire de séquestrer les polluants toxiques dans leurs feuilles ou leurs racines. Ces recherches ont permis d'apporter des solutions originales pour la restauration écologique des sols et la décontamination des systèmes aquatiques à l'aide d'espèces végétales exotiques envahissantes mortes. Afin de les rendre pérennes et économiquement viables, ces solutions ont été valorisées à travers le concept de l'écocatalyse, à l'interface de l'écologie et de la chimie.

Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network.

The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.

Loss of microbial diversity increases methane emissions and arsenic release in paddy soils.

Microorganisms are vital to the emission of greenhouse gases and transforming pollutants in paddy soils. However, the impact of microbial diversity loss on anaerobic methane (CH4) oxidation and arsenic (As) reduction under flooded conditions remains unclear. In this study, we inoculated microbial suspensions into natural As-contaminated paddy soils using a dilution approach (untreated, 10-2, 10-4, 10-6, 10-8 dilutions) to manipulate microbial diversity levels. The results revealed that the 10-4 and 10-6 dilutions resulted in the highest CH4 emissions (97.0 µmol and 102.3 µmol) compared to untreated groups (27.6 µmol). However, anaerobic CH4 oxidation was not observed in 10-4 dilution groups and higher dilutions, suggesting the loss of diversity inhibited the natural reduction of CH4. Moreover, the porewater As concentration in the dilution groups was 1.8-8.2 times greater than in the untreated groups. The loss of microbial diversity promoted the reductive dissolution of iron (Fe) minerals bearing As, leading to increased concentrations of Fe(II) and dissolved organic carbon (DOC), which further enhanced As release (Fe(II), R = 0.9, p < 0.001) (DOC, R = 0.8, p < 0.001) from soil to porewater. However, CH4-dependent As(V) reduction was almost entirely inhibited under diversity loss. The decline in microbial diversity increased the relative abundances of methanogens (e.g., Methanobacterium and Methanomassiliicoccus), Fe(III)/As(V)-reducing bacteria (e.g., Bacillus, Clostridium_sensu_stricto_10, and Geobacter), and the related functional genes (i.e., mcrA and Geo). These findings suggest that microbial diversity is critical for specialized soil processes, highlighting the detrimental effects of biodiversity loss on CH4 emissions and As release in As-contaminated paddies.

Declining glacier cover drives changes in aquatic macroinvertebrate biodiversity in the Cordillera Blanca, Perú.

Ongoing climate change threatens the biodiversity of glacier-fed river ecosystems worldwide through shifts in water availability and timing, temperature, chemistry, and channel stability. However, tropical glacier-fed rivers have received little attention compared to those in temperate and Arctic biomes, despite their unique biodiversity potentially responding differently due to additional stress from higher altitude locations thus lower oxygen availability, diurnal freeze-thaw cycles, and annual monsoon rainfall disturbances. However, tropical glacier-fed rivers have received little attention compared to those in temperate and Arctic biomes, despite their unique biodiversity potentially responding differently due to additional stress from higher altitude locations thus lower oxygen availability, diurnal freeze-thaw cycles, and annual monsoon rainfall disturbances. This study quantified aquatic biodiversity responses to decreasing glacier cover in the Cordillera Blanca range of the Peruvian Andes. Ten rivers were studied along a gradient of decreasing glacier cover in the Parón, Huaytapallana, and Llanganuco basins, with a specific focus on macroinvertebrates and physicochemical parameters in both the dry and wet seasons. We found higher temperatures, more stable and lower turbidity rivers as glacier cover decreased, which were related significantly to higher local diversity and lower ß-diversity. Analysis of similarity revealed significant differences in the macroinvertebrate community among rivers with high, medium, or low glacier cover, illustrating turnover from specialists to generalists as glacial influence decreased. Redundancy analysis demonstrated that there were more species found to prefer stable beds and water temperatures in medium and low glacier cover in a catchment rivers. However, certain taxa in groups such as Paraheptagyia, Orthocladiinae, Anomalocosmoecus, and Limonia may be adapted to high glacial influence habitats and at risk of glacier retreat. Although species composition was different to other biomes, the Cordillera Blanca rivers showed similar benthic macroinvertebrate biodiversity responses to glacier retreat, supporting the hypothesis that climate change will have predictable effects on aquatic biodiversity in mountain ranges worldwide.

Establishing Silphids in the invertebrate DNA toolbox: a proof of concept.

Environmental DNA (eDNA) analyses are an increasingly popular tool for assessing biodiversity. eDNA sampling that uses invertebrates, or invertebrate DNA (iDNA), has become a more common method in mammal biodiversity studies where biodiversity is assessed via diet analysis of different coprophagous or hematophagous invertebrates. The carrion feeding family of beetles (Silphidae: Coleoptera, Latreille (1807)), have not yet been established as a viable iDNA source in primary scientific literature, yet could be useful indicators for tracking biodiversity in forested ecosystems. Silphids find carcasses of varying size for both food and reproduction, with some species having host preference for small mammals; therefore, iDNA Silphid studies could potentially target small mammal communities. To establish the first valid use of iDNA methods to detect Silphid diets, we conducted a study with the objective of testing the validity of iDNA methods applied to Silphids using both Sanger sequencing and high throughput Illumina sequencing. Beetles were collected using inexpensive pitfall traps in Alberta, Michigan in 2019 and 2022. We successfully sequenced diet DNA and environmental DNA from externally swabbed Silphid samples and diet DNA from gut dissections, confirming their potential as an iDNA tool in mammalian studies. Our results demonstrate the usefulness of Silphids for iDNA research where we detected species from the genera Anaxyrus, Blarina, Procyon, Condylura, Peromyscus, Canis, and Bos. Our results highlight the potential for Silphid iDNA to be used in future wildlife surveys.

Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces.

Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.

Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework.

Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of the taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.

Brown trout in Oder estuary tributaries: genetic structure, stocking, and admixture.

Several rivers that are tributaries of the Oder estuary are inhabited by Salmo trutta L, the most important of which are Ina, Gowienica, and Wolczenica. Both forms of the species, sea trout and resident brown trout, are present. All rivers are traditionally stocked with either sea trout from the neighboring Pomeranian river Rega basin or resident brown trout from various locations. To examine populations in these rivers in terms of genetic structure, genetic diversity, and origin, they were analyzed using 13 microsatellite loci. Relatedness was also assessed for fish stocked in the same year. The obtained genotypes were compared with breeding stocks used for stocking in Poland. The analyses revealed a significant genetic distance between adult individuals from Ina and Rega Rivers and fish caught during electrofishing. Strong kinship relationships were identified in the sampled areas, with high proportions of fish originating from stocking and their dominance in numbers over wild juveniles, primarily in smaller tributaries. Additionally, clear separation in the origin of stocked individuals was observed. Adult trout from Ina and Rega are genetically closer to northern brown trout lineages, providing crucial information for the management and biodiversity conservation of Polish Salmo trutta populations.

Fire impacts on the biology of stream ecosystems: A synthesis of current knowledge to guide future research and integrated fire management.

Freshwater ecosystems host disproportionately high biodiversity and provide unique ecosystem services, yet they are being degraded at an alarming rate. Fires, which are becoming increasingly frequent and intense due to global change, can affect these ecosystems in many ways, but this relationship is not fully understood. We conducted a systematic review to characterize the literature on the effects of fires on stream ecosystems and found that (1) abiotic indicators were more commonly investigated than biotic ones, (2) most previous research was conducted in North America and in the temperate evergreen forest biome, (3) following a control-impact (CI) or before-after (BA) design, (4) predominantly assessing wildfires as opposed to prescribed fires, (5) in small headwater streams, and (6) with a focus on structural and not functional biological indicators. After quantitatively analyzing previous research, we detected great variability in responses, with increases, decreases, and no changes being reported for most indicators (e.g., macroinvertebrate richness, fish density, algal biomass, and leaf decomposition). We shed light on these seemingly contradicting results by showing that the presence of extreme hydrological post-fire events, the time lag between fire and sampling, and whether the riparian forest burned or not influenced the outcome of previous research. Results suggest that although wildfires and the following hydrological events can have dramatic impacts in the short term, most biological endpoints recover within 5-10 years, and that detrimental effects are minimal in the case of prescribed fires. We also detected that no effects were more often reported by BACI studies than by CI or BA studies, raising the question of whether this research field may be biased by the inherent limitations of CI and BA designs. Finally, we make recommendations to help advance this field of research and guide future integrated fire management that includes the protection of freshwater ecosystems.

Insufficient and biased representation of species geographic responses to climate change.

The geographic redistributions of species due to a rapidly changing climate are poised to perturb ecological communities and significantly impact ecosystems and human livelihoods. Effectively managing these biological impacts requires a thorough understanding of the patterns and processes of species geographic range shifts. While substantial recent redistributions have been identified and recognized to vary by taxon, region, and range geometry, there are large gaps and biases in the available evidence. Here, we use the largest compilation of geographic range change observations to date, comprised of 33,016 potential redistributions across 12,009 species, to formally assess within- and cross-species coverage and biases and to motivate future data collection. We find that species coverage varies strongly by taxon and underrepresents species at high and low latitudes. Within species, assessments of potential redistributions came from parts of their geographic range that were highly uneven and non-representative. For most species and taxa, studies were strongly biased toward the colder parts of species' distributions and thus significantly underrepresented populations that might get pushed beyond their maximum temperature limits. Coverage of potential leading and trailing geographic range edges under a changing climate was similarly uneven. Only 8% of studied species were assessed at both high and low latitude and elevation range edges, with most only covered at one edge. This suggests that substantial within-species biases exacerbate the considerable geographic and taxonomic among-species unevenness in evidence. Our results open the door for a more quantitative accounting for existing knowledge biases in climate change ecology and a more informed management and conservation. Our findings offer guidance for future data collection that better addresses information gaps and provides a more effective foundation for managing the biological impacts of climate change.

Ten lessons learned from the mass digitisation of a herbarium collection.

Worldwide, herbaria maintain collections of reference specimens representing global plant diversity. These collections are a valuable resource for fundamental botanical research and applied scientific research across various disciplines, and play a significant role in addressing major societal challenges such as biodiversity conservation. The digitisation of herbarium specimens and their online dissemination is one of the most important recent developments in the curation of these collections. Digitisation significantly enhances access to the collections for the research community and facilitates large-scale analysis of biodiversity data. Digitisation also provides a means for preserving the physical specimens, as it reduces the need for handling and transportation. Rapid technological developments have greatly accelerated the rate of databasing and digital imaging of collections. Meise Botanic Garden recently completed a six-year project to mass digitise its herbarium collections of about 3 million specimens mounted on sheets and through this process we have learned valuable lessons. We have captured our experience in 10 recommendations for other collection-holding institutions to take inspiration from as they start planning their own digitisation efforts. We also present case studies where we delve deeper into certain topics as examples.

Forest Orchids under Future Climate Scenarios: Habitat Suitability Modelling to Inform Conservation Strategies.

Orchidaceae is one of the largest and most diverse families of flowering plants in the world but also one of the most threatened. Climate change is a global driver of plant distribution and may be the cause of their disappearance in some regions. Forest orchids are associated with specific biotic and abiotic environmental factors, that influence their local presence/absence. Changes in these conditions can lead to significant differences in species distribution. We studied three forest orchids belonging to different genera (Cephalanthera, Epipactis and Limodorum) for their potential current and future distribution in a protected area (PA) of the Northern Apennines. A Habitat Suitability Model was constructed for each species based on presence-only data and the Maximum Entropy algorithm (MaxEnt) was used for the modelling. Climatic, edaphic, topographic, anthropogenic and land cover variables were used as environmental predictors and processed in the model. The aim is to identify the environmental factors that most influence the current species distribution and the areas that are likely to contain habitats suitable for providing refuge for forest orchids and ensuring their survival under future scenarios. This will allow PA authorities to decide whether to invest more resources in conserving areas that are potential refuges for threatened species.

Socioeconomic Disparities in Urban Forest Diversity and Structure in Green Areas of Santiago de Chile.

Urban trees enhance biodiversity, provide ecosystem services, and improve quality of life in cities. Despite their benefits, trees are not distributed equitably, and many cities exhibit a "luxury effect". Given the importance of public green space for providing access to urban tree benefits, we investigated the relationship between socioeconomic level and tree diversity and structure in 60 green areas in Santiago de Chile. Species richness and total tree abundance did not significantly vary among socioeconomic levels; however, a differential effect was found according to species origin. Introduced tree species exhibited similar abundance and species richness across socioeconomic levels, but native tree species were more abundant and richer in higher socioeconomic level areas compared to lower ones. Tree cover was higher in the high and medium socioeconomic level areas than in the low socioeconomic level area. A higher average DBH was found in the medium socioeconomic level area, which may be explained by older neighborhoods and a legacy of the luxury effect. Our findings reveal that socioeconomic groups are associated with differences in tree cover, width, and the number of native species in public green areas. Consequently, urban residents have different provisions of ecosystem services and opportunities to interact with natural heritage. Increasing the amount of tree cover and native species available to vulnerable groups will reduce disparities.

Biogeographical distribution and community assembly of Myxococcota in mangrove sediments.

BACKGROUND: Myxococcota, characterized by their distinct social lifestyles, are widely distributed micro-predators in global sediments. They can feed on a wide range of bacterial, archaeal, and fungal prey. Myxococcota are capable of producing diverse secondary metabolites, playing key roles in microbial food webs, and regulating the microbial community structures in different ecosystems. However, Myxococcota are rarely pure cultured due to the challenging and stringent culturing conditions. Their natural distribution, niche differentiation, and predator-prey relationships in a specific habitat are poorly understood. RESULTS: In this study, we conducted a comprehensive analysis of the 16S rRNA gene sequence data from public databases and our collection. We compared the abundance, diversity, and distribution patterns of Myxococcota in various habitats, with a specific focus on mangroves. We found that Myxococcota accounted for 1.45% of the total prokaryotes in global sediments based on the abundance of 16S rRNA genes. Myxococcota are abundant and diverse in mangrove sediments. They tend to be more generalistic in mangroves than in other habitats due to their wide niche breadth. Besides, the deterministic processes (variable selection) influenced the assembly of mangrove Myxococcota communities significantly more than stochastic processes. Further, we determined that environmental factors explained a greater amount of total community variation in mangrove Myxococcota than geographical variables (latitude and sediment depth). In the end, through the analysis of microbial co-occurrence networks, Myxococcota emerges as a key component and functions as a connector in the mangrove microbial community. CONCLUSIONS: Our study enhances comprehension of mangrove Myxococcota's biogeography, assembly patterns, driving factors, and co-occurrence relationships, as well as highlights their unique niche and ecological importance in mangrove sediments.

Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be , has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.