Centering microbes in the emerging role of integrative biology in understanding environmental change

Synopsis We argue that the current environmental changes stressing the Earth’s biological systems urgently require study from an integrated perspective to reveal unexpected, cross-scale interactions, particularly between microbes and macroscale phenomena. Such interactions are the basis of a mechanistic understanding of the important connections between deforestation and emerging infectious disease, feedback between ecosystem disturbance and the gut microbiome, and the cross-scale effects of environmental pollutants. These kinds of questions can be answered with existing techniques and data, but a concerted effort is necessary to better coordinate studies and data sets from different disciplines to fully leverage their potential.

Microbial colonisation, the missing link: from airborne dispersal to integration within the soil community.

BackgroundGlobal dispersal of microorganisms primarily occurs through airborne transport. Airborne microorganisms can travel thousands of kilometres and be deposited in the most remote places on Earth, from the Arctic to Antarctica, with the potential of invasion and colonisation. The first stage of microbial colonisation is deposition into a new ecosystem. However, how and under what circumstances such deposited microorganisms might successfully colonise a new environment is yet to be determined. Using the Arctic snowpack as a model system, we investigated the colonisation potential of snow derived bacteria deposited onto Arctic soils during and after snowmelt using laboratory-based microcosm experiments set-up to mimic realistic environmental conditions. We tested different melting rate scenarios to evaluate the influence of increased precipitation (via the increase of bacterial inputs and ecosystem disturbance) as well as the influence of soil pH (as the key driver of soil diversity) on bacterial communities and on the colonisation potential.Results We observed several candidate colonisations in all experiments; however, the number of potentially successful colonisation was higher in acidoneutral soils, at the average snowmelt rate measured in the Arctic. While the higher melt rate increased the total number of potentially invading bacteria, it did not promote colonisation. Instead, persistence decreased with time and most potential colonists were not identified by the end of the experiments. On the other hand, soil pH appeared as a determinant factor impacting invasion and subsequent colonisation. In acidic and alkaline soils, bacterial persistence with time was lower than in acidoneutral soils, as was the number of potentially successful colonisations. ConclusionsThis is the first study to investigate bacterial colonisation using the snowpack as a model system, and to demonstrate the low rate of potentially successful colonisations of soil by invading bacteria. It suggests that local soil properties might have a greater influence on the colonisation outcome than increased precipitation or ecosystem disturbance.

Sustained volcanic impact and ecosystem disturbance over continental Europe during the Early Holocene

Estimating the environmental and societal impact of recent volcanic eruptions is a task aided by direct measurements and historical sources. Beyond the reach of first-hand accounts, our understanding of pre-historic volcanism is often hindered by the dating uncertainties inherent to stratigraphic archives. Here, we minimise this source of error by analysing the annually laminated sequences of two European lakes. We focus on environmental transformations that occurred in the decades preceding and following the deposition of the Icelandic Saksunarvatn tephra, dated between ca. 10,300 and 10,200 cal. BP. Evidence for continuous eruptive activity pre-dates the tephra deposition by nearly two decades, revealing a period of sustained volcanism and its effects on aquatic and terrestrial ecosystems. These results provide a new insight into the spatial and temporal effects of clustered volcanic eruptions. As such, they might prove useful to refine the simulation of volcanic forcing on continental ecosystems and to evaluate the resilience of prehistoric societies against sudden environmental downturns.

Soil Nematode Fauna and Microbial Characteristics in an Early-Successional Forest Ecosystem

Windstorms can often decrease the diversity of native local biota in European forests. The effects of windstorms on the species richness of flora and fauna in coniferous forests of natural reserves are well established, but the effects on biotas in productive deciduous forests have been less well studied. We analyzed the impact of windstorms on the diversity and abundance of soil nematode communities and microbial activity and their relationships with the succession of plant species and basic soil physicochemical properties 12 and 36 months after a windstorm in Fagus sylvatica forests. The relationships were investigated in cleared early-successional forest ecosystems and at undamaged forest sites as a control. The windstorm significantly affected total nematode abundance, number of nematode species, and the diversity and abundance of all nematode functional guilds, but no functional guilds disappeared after the disturbance. The abundance of several nematode taxa but not total nematode abundance was positively correlated with soil-moisture content. Indices of the nematode communities were inconsistent between sites due to their variable ability to identify ecosystem disturbance 12 months after the storm. In contrast, the metabolic activity of various functional groups identified ecosystem disturbance well throughout the study. Positive correlations were identified between the number of plant parasites and soil-moisture content and between carnivore abundance and soil pH. Positive mutual links of some nematode genera (mainly plant parasites) with the distribution of dominant grasses and herbs depended on the habitat. In contrast, microbial activity differed significantly between disturbed and undisturbed sites up to 36 months after the storm, especially soil basal respiration, N mineralization, and microbial biomass. Our results indicated different temporal responses for two groups of soil organisms to the destruction of the tree canopy. Soil nematodes reacted immediately, but changes in the microbial communities were visible much later after the disturbance.