Ecological resilience of soil microbial communities

Het meest bijzondere kenmerk van levende ecosystemen is waarschijnlijk hun vermogen zich aan te passen aan hun omgeving, ook onder ogenschijnlijk onoverkomelijke obstakels. Dit verschijnsel noem ik “ecological resilience”. Dit proefschrift richt zich op de kloof tussen de theoretische en experimentele kennis over het herstelproces na verstoring van microbiële bodemgemeenschappen.The soil microbial system is largely responsible for the maintenance of terrestrial nutrient cycles. The soil microbiome is among the most diverse and dynamic systems on the planet, and the provision of these services is largely dependent on the capacity of microbial communities to function as a unit. Predicted changes to global climate and increasing anthropogenic pressures pose a potential threat to microbial communities, as changes in precipitation patterns and temperature beyond the community’s adaptive range may change survival, dominance, and interaction patterns among community members, potentially affecting the community’s ability to provide ecosystem services and recover from future disturbances. This may be exacerbated if the soils have been previously disturbed by, for example intensive land use.This thesis aims to discover whether resilience can be lost from the soil microbial system by multiple disturbances, and provide mechanistic insights as to the processes behind this phenomenon, as well as its implications for the maintenance of terrestrial ecosystem services in a changing environment. Through two comprehensive microcosm and mesocosm experiments, I study the effect of disturbance on the niche structure of microbial communities. This thesis targets the following questions:Does the soil microbiota exhibit a sequential, predictable recovery, similar to secondary succession in macro-ecology?Are successional patterns affected by the soil’s legacy?Does intensive agriculture result in soils with “disturbed” legacies?Are soils exposed to intensive agriculture more vulnerable to changes in precipitation patterns? Is the integrity of the nitrogen cycling more vulnerable in disturbed soils

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life

Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research

COVID-19 alters human microbiomes: a meta-analysis

International audienceIntroduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world’s population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential.Methods We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries.Results Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma .Discussion Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota

Diversity of plasmodial slime molds (myxomycetes) in coastal, mountain, and community forests of Puerto Galera, Oriental Mindoro, the Philippines

AbstractNo profiling of diversity of myxomycetes has ever been conducted in one of the biodiversity hotspot areas in the Philippine archipelago, and this necessitates a swift survey of myxomycetes in Puerto Galera, Oriental Mindoro. An assessment of diversity of myxomycetes collected from seven collecting points of three different forest types in the study area showed a total of 926 records of myxomycetes. Of which, 42 morphospecies belonging to 16 genera are reported in this study. Species richness of myxomycetes was higher in collecting points that were found in inland lowland mountain forests, but the most taxonomically diverse species was found in coastal forests. Myxomycete species, namely, Arcyria cinerea, Diderma hemisphaericum, Physarum echinosporum, Lamproderma scintillans, and Stemonitis fusca, were found in all the collecting points. Manmade disturbances and forest structure may affect the occurrence of myxomycetes

All together now : limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences

The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data

A history of extreme disturbance affects the relationship between the abundances of nitrifiers in soil

To understand how and to what extent single or multiple perturbations can alter the relationships between the abundances of different nitrifier groups and nitrification, soil microcosms were exposed to six disturbance treatments: a heat shock, cold shock, or control conditions applied to undisturbed soils or to soils that had previously been subjected to a first heat shock. We monitored the recovery of the abundances of four main nitrifier groups (ammonia-oxidizing archaea and bacteria, AOA and AOB, respectively, andNitrobacterandNitrospiranitrite oxidizers) as well as nitrification activity for 25 days. AOA were sensitive to cold shocks, whereas AOB were not; the latter were sensitive to heat shock. Despite the variations, both groups were resilient to the first disturbance. In contrast,Nitrobacterwas affected by both disturbances, whereasNitrospirawas resistant to both shocks. Prior exposure to a heat shock affected each group's responses as well as the relationships between them. For example, AOB were more vulnerable to heat shock in pre-exposed soils, whereas under the same circumstances, AOA were resilient. Nitrification activity was resistant to the first disturbances, but a legacy effect was observed, and nitrification was highest in Heat-Heat and lowest in Heat-Cold treatments. Overall, our study shows that within soil nitrifiers, temporal patterns and legacy effects interact to result in complex disturbance responses

Tropical Oceanic Causes of Interannual to Multidecadal Precipitation Variability in Southeast South America over the Past Century

Observations, atmosphere models forced by historical SSTs, and idealized simulations are used to determine the causes and mechanisms of interannual to multidecadal precipitation anomalies over southeast South America (SESA) since 1901. About 40% of SESA precipitation variability over this period can be accounted for by global SST forcing. Both the tropical Pacific and Atlantic Oceans share the driving of SESA precipitation, with the latter contributing the most on multidecadal time scales and explaining a wetting trend from the early midcentury until the end of the last century. Cold tropical Atlantic SST anomalies are shown to drive wet conditions in SESA. The dynamics that link SESA precipitation to tropical Atlantic SST anomalies are explored. Cold tropical Atlantic SST anomalies force equatorward-flowing upper-tropospheric flow to the southeast of the tropical heating anomaly, and the vorticity advection by this flow is balanced by vortex stretching and ascent, which drives the increased precipitation. The 1930s Pampas Dust Bowl drought occurred, via this mechanism, in response to warm tropical Atlantic SST anomalies. The atmospheric response to cold tropical Pacific SSTs also contributed. The tropical Atlantic SST anomalies linked to SESA precipitation are the tropical components of the Atlantic multidecadal oscillation. There is little evidence that the large trends over past decades are related to anthropogenic radiative forcing, although models project that this will cause a modest wetting of the climate of SESA. As such, and if the Atlantic multidecadal oscillation has shifted toward a warm phase, it should not be assumed that the long-term wetting trend in SESA will continue. Any reversal to a drier climate more typical of earlier decades would have clear consequences for regional agriculture and water resources