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

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

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