Initiating a collaborative monitoring system to survey Maltese orchids

Orchids have always garnered the interest of enthusiastic amateurs and nonprofessional researchers as a charismatic species group and have become a flagship for Mediterranean flora. At the same time they are a decent indicator for biodiversity and environmental quality through their association with specific pollinators and mycorrhizal fungi. Historical records for orchids occurring in the Maltese Islands number some 30 different species, but there is little to no comprehensive data on their abundance and distribution.peer-reviewe

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Cities and their effects on free-living and host-associated microbes

Mikrobit ovat oleellisen tärkeitä elämälle maapallolla, ja niitä esiintyy vapaina ympäristössä tai isäntäorganismeissa tukien ekosysteemien ja/tai isäntien normaalia toimintaa. Ihminen vaikuttaa lähes kaikkiin planeettamme elinympäristöihin aiheuttaen niiden häviämistä ja huonontumista (mukaan lukien kaupunkien rakentaminen) sekä ympäristöjen saastumista ja ilmastonmuutosta. Mikrobiyhteisöjen (kutsutaan myös mikrobiotaksi, mukaan lukien bakteerit ja sienet) odotetaan reagoivan näihin ihmisen aiheuttamiin valintapaineisiin sopeutumalla muuttuvaan ympäristöön. Siten ihmisen aiheuttamat muutokset ympäristössä voivat muovata mikrobiyhteisöjä (sekä vapaasti eläviä että isäntiin liittyviä) muuttaen mikrobi-yhteisöjen vaikutuksia ekosysteemeissä ja isännissä. Väitöskirjassani tutkin ihmistoiminnan vaikutuksia ympäristössä vapaasti eläviin ja luonnonvaraisissa isäntäeläimissä esiintyviin mikrobiyhteisöihin käyttämällä erilaisia tutkimusasetelmia, mukaan lukien laaja-alaiset poikkileikkausaineistot ja kokeelliset työt sekä DNA-metaviivakoodaus ja isotooppianalyysit. Väitöskirjatyöni tavoitteena oli määrittää kuinka kaupungistuminen vaikuttaa (1) metsämaaperän ja (2) jyrsijöiden (metsämyyrän) suoliston bakteeri- ja sieniyhteisöihin. Lisäksi tarkastelin, kuinka (3) metsämyyrän suoliston mikrobiota säilyy muuttumattomana (resistenssi) tai muuttuu (plastisuus) vastaamaan uutta ympäristöä elinympäristön vaihtumisen jälkeen (isännän siirto kaupunkien ja maaseudun metsien välillä). Tulosteni perusteella molemmat, sekä 1) metsän maaperän mikrobisto, että 2) metsämyyrän suolistomikrobisto eroavat kaupunkimetsien ja kaupunkien ulkopuolisten metsien välillä. Erityisesti erot maaperän happamuudessa ja jyrsijöiden ruokavaliossa tunnistettiin tärkeiksi tekijöiksi maaperän ja metsämyyrän suolen mikrobiotan muovautumisessa. Lisäksi havaitsin, että elinympäristön muutosta edeltävä ympäristö (resistenssi) ja uusi ympäristö (plastisuus) vaikuttavat suoliston mikrobiotan koostumukseen luonnonvaraisessa jyrsijässä. Väitöskirjani tulokset osoittavat, että kaupunkiluonto vaikuttaa mikrobiyhteisöihin kahdessa eri järjestelmässä ja osoittavat täten kaupungistumisen kauaskantoiset vaikutukset mikrobien elämänmuotoihin.Microbes are essential for all life on Earth and can be found in the environment or in association with host organisms, where they perform essential tasks either needed for the health of ecosystems or their hosts. Humans impact almost every habitat on our planet through various processes such as loss and degradation of habitat including urban development, pollution and climate change. As a result, microbial communities (also referred to as the microbiota, including bacteria and fungi) are expected to respond to these selective pressures by adjusting to a changing environment. In this way, human alterations of the natural landscape have the power to impact diverse microbiota (both free-living and host-associated), that in turn may affect the delivery of the services they provide to ecosystems and their hosts. Using an innovative combination of extensive cross-sectional surveys, longitudinal field experiments, DNA metabarcoding techniques and stable isotope analyses, my doctoral thesis focuses on the impacts of human activities on free-living and host-associated microbiota, with the aim to quantify the specific variation in bacterial and fungal (1) forest soil and (2) rodent (the bank vole) gut microbial communities in the context of urbanisation, and (3) the level of resistance (i.e., mechanism by which microbial communities do not change after habitat alteration) and plasticity (i.e., mechanism by which microbial communities change to match the novel environment after habitat alteration) displayed by the rodent bacterial gut microbiota in response to a change in the environment (host transfer between urban and rural forests). I found both (1) urban soil microbiota and (2) urban rodent gut microbiota to be distinct from those occurring in forests that are less impacted by urbanisation. Notably, soil pH and a dietary switch were identified as important factors in shaping the soil and bank vole gut microbiota, respectively. Additionally, I found that (3) both past (resistance) and present (plasticity) habitats influence the gut microbiota composition in a wild rodent. This thesis summarises the effects of the urban environment on microbial communities in two different systems and hereby demonstrates the far-reaching effects of urbanisation on microbial life forms

Defining gut mycobiota for wild animals : a need for caution in assigning authentic resident fungal taxa

Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host’s diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress this problem, we propose some strategies to filter the taxa identified within an apparent gut mycobiota based on an assessment of host ecology and fungal traits. Consideration of the different sources and roles of fungi present within the gastrointestinal tract should facilitate a more precise understanding of the causes and consequences of variation in wild animal gut mycobiota composition.peerReviewe

Scholier et al. Supplementary Information & Methods from Effects of past and present habitat on the gut microbiota of a wild rodent

Methods & Tables S1-S8 & Figures S1-S

Ecosystem health and planetary well-being

Healthy ecosystems support the well-being of all organisms on Earth. Yet, the overexploitation of natural resources for human needs and profit has resulted in widespread ecosystem degradation, loss of biodiversity, and climate emergency, which pose fundamental threats to planetary well-being. Impoverished ecosystems may become dysfunctional and fail to provide for the needs of many organisms, including humans and wildlife. Changes in ecosystem functioning and wildlife distributions affect the prevalence and spread of pathogens, with consequences for the health and well-being of human and wildlife communities alike. Increasing contact between humans and domestic and wild animals enable pathogen spillover, while global trade and travel distribute pathogens to new areas. Human activities thus provide favourable conditions for pandemics and trigger cascading consequences for ecosystems worldwide. A better integration of ecosystem health into public health and conservation planning could alleviate disease burden and improve well-being of all organisms on the planet.peerReviewe

Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils

Anthropogenic changes to land use drive concomitant changes in biodiversity, including that of the soil microbiota. However, it is not clear how increasing intensity of human disturbance is reflected in the soil microbial communities. To address this issue, we used amplicon sequencing to quantify the microbiota (bacteria and fungi) in the soil of forests (n=312) experiencing four different land uses, national parks (set aside for nature conservation), managed (for forestry purposes), suburban (on the border of an urban area) and urban (fully within a town or city), which broadly represent a gradient of anthropogenic disturbance. Alpha diversity of bacteria and fungi increased with increasing levels of anthropogenic disturbance, and was thus highest in urban forest soils and lowest in the national parks. The forest soil microbial communities were structured according to the level of anthropogenic disturbance, with a clear urban signature evident in both bacteria and fungi. Despite notable differences in community composition, there was little change in the predicted functional traits of urban bacteria. By contrast, urban soils exhibited a marked loss of ectomycorrhizal fungi. Soil pH was positively correlated with the level of disturbance, and thus was the strongest predictor of variation in alpha and beta diversity of forest soil communities, indicating a role of soil alkalinity in structuring urban soil microbial communities. Hence, our study shows how the properties of urban forest soils promote an increase in microbial diversity and a change in forest soil microbiota composition.peerReviewe

Chimpanzees surviving in a fragmented high‐altitude forest landscape of the Congolese Albertine Rift

This paper documents a community of eastern chimpanzees (Pan troglodytes schweinfurthii Giglioli, 1872) inhabiting three relict forest fragments situated on the Lake Albert escarpment, down the Ituri highlands, of eastern Democratic Republic of the Congo (DRC). The area explored had a combined forested surface of ±18.15 km2 in 2017, shrinking by 1.2% per year between 2010 and 2015. Between 2015 and 2017, we found 160 chimpanzee nests along 37.6 km of pilot walks, some up to 2,000 m altitude. Another 123 nests logged along 6.7 km transects led to an estimate of chimpanzee density of 4.62 weaned individuals per square kilometer of forest habitat. Camera‐trap images and direct observations revealed that this community is comprised of a minimum of 42 weaned individuals, which translates into an estimated density of 2.3 chimpanzees per square kilometer. The increasing rate of forest degradation threatens to erode the cultural and genetic diversity of nonhuman primates in eastern DRC; the local people however exhibit willingness to establish a community managed reserve. We hope that this report will lead to the recognition of this site as a Chimpanzee Conservation Unit, facilitating further research in these “Relict Altitude Forests Fragments of the Albert Lake Escarpment” (or RAFALE landscape) and the Ituri highlands where other undocumented chimpanzee communities occur.peerReviewe

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale