Moisture as a regulator of microbial life in soil

Climate change models predict an increase in the intensity and frequency of drought periods as well as precipitation events. Moisture and its fluctuations have a large impact on soil microorganisms, which are key drivers of the terrestrial carbon (C) cycle. When there is a drought period followed by a rainfall event there is a big CO2 release from soil to the atmosphere, which can dominate the C budget of some ecosystems. During this period, respiration and microbial growth have been shown to be transiently uncoupled. Earlier studies showed that microbial growth and respiration can respond in two different ways upon rewetting, resulting in differences in microbial carbon use efficiency (i.e., the fraction of used C allocated to growth) and resilience (i.e., the ability of microbial growth to recover to levels before the soils were disturbed). An understanding of how moisture and its fluctuations impact soil microbial communities is thus key to predict terrestrial ecosystem responses to ongoing global change. The aim of this thesis was to understand how soil microbial communities, and the processes they regulate, are affected by moisture and moisture fluctuations. Specifically, the objectives were to understand (1) what determines the two different microbial response patterns upon rewetting, (2) how the historical conditions microbial communities have been exposed shape their responses to drought and drying and rewetting (DRW) events, and (3) the differences in responses to drought and DRW events between the two major microbial groups, bacteria and fungi. It was found that (1) the conditions of the DRW disturbance as well as the microbial community’s ability to cope with DRW could affect microbial responses to DRW. In addition, individual studies did not show that historical conditions could shape microbial drought tolerance and responses to DRW. However, when taking all the results together with other preliminary results that cover a wider climate range, (2) historical conditions that microbial communities had been exposed to were important. A history of drier condition, as well as a history of higher soil disturbance resulted in more efficient and resilient responses upon rewetting. These results might be due to either (i) microbial adjustment to better cope with disturbances or (ii) differences in resource availability and quality due to differences in climate history or aboveground community. Finally, (3) fungi tolerated drought better than bacteria, and could be equally or more resilient than bacteria after a DRW event. In summary, to better predict how terrestrial ecosystems will respond to the increase of drought periods and precipitation events, ecosystem models should take into account that bacteria and fungi are differently affected by moisture. In addition, the harshness of the DRW disturbance as well as the previous conditions that microbial communities have been exposed to are important to determine their response to drought and DRW events as well as their carbon use efficiency

Partial drying accelerates bacterial growth recovery to rewetting

Fluctuations in soil moisture create drying-rewetting events affecting the activity of microorganisms. Microbial responses to drying-rewetting are mostly studied in soils that are air-dried before rewetting. Upon rewetting, two patterns of bacterial growth have been observed. In the Type 1 pattern, bacterial growth rates increase immediately in a linear fashion. In the Type 2 pattern, bacterial growth rates increase exponentially after a lag period. However, soils are often only partially dried. Partial drying (higher remaining moisture content before rewetting) may be considered a less harsh treatment compared with air-drying. We hypothesized that a soil with a Type 2 response upon rewetting air-dried soil would transform into a Type 1 response if dried partially before rewetting. Two soils were dried to a gradient of different moisture content. Respiration and bacterial growth rates were then measured before and during 48 h after rewetting to 50% of water holding capacity (WHC). Initial moisture content determined growth and respiration in a sigmoidal fashion, with lowest activity in air-dried soil and maximum above ca. 30% WHC. Partial drying resulted in shorter lag periods, shorter recovery times and lower maximum bacterial growth rates after rewetting. The respiration after rewetting was lower when soil was partially dried and higher when soils were air-dried. The threshold moisture content where transition from a Type 2 to a Type 1 response occurred was about 14% WHC, while >30% WHC resulted in no rewetting effect. We combine our result with other recent reports to propose a framework of response patterns after drying-rewetting, where the harshness of drying determines the response pattern of bacteria upon rewetting dried soils

Simulated rhizosphere deposits induce microbial N-mining that may accelerate shrubification in the subarctic

Climate change is exposing high-latitude systems to warming and a shift towards more shrub-dominated plant communities, resulting in increased leaf-litter inputs at the soil surface, and more labile root-derived organic matter (OM) input in the soil profile. Labile OM can stimulate the mineralization of soil organic matter (SOM); a phenomenon termed “priming.” In N-poor subarctic soils, it is hypothesized that microorganisms may “prime” SOM in order to acquire N (microbial N-mining). Increased leaf-litter inputs with a high C/N ratio might further exacerbate microbial N demand, and increase the susceptibility of N-poor soils to N-mining. We investigated the N-control of SOM mineralization by amending soils from climate change–simulation treatments in the subarctic (+1.1°C warming, birch litter addition, willow litter addition, and fungal sporocarp addition) with labile OM either in the form of glucose (labile C; equivalent to 400 µg C/g fresh [fwt] soil) or alanine (labile C + N; equivalent to 400 µg C and 157 µg N/g fwt soil), to simulate rhizosphere inputs. Surprisingly, we found that despite 5 yr of simulated climate change treatments, there were no significant effects of the field-treatments on microbial process rates, community structure or responses to labile OM. Glucose primed the mineralization of both C and N from SOM, but gross mineralization of N was stimulated more than that of C, suggesting that microbial SOM use increased in magnitude and shifted to components richer in N (i.e., selective microbial N-mining). The addition of alanine also resulted in priming of both C and N mineralization, but the N mineralization stimulated by alanine was greater than that stimulated by glucose, indicating strong N-mining even when a source of labile OM including N was supplied. Microbial carbon use efficiency was reduced in response to both labile OM inputs. Overall, these findings suggest that shrub expansion could fundamentally alter biogeochemical cycling in the subarctic, yielding more N available for plant uptake in these N-limited soils, thus driving positive plant–soil feedbacks

Pathways from research to sustainable development: insights from ten research projects in sustainability and resilience

Drawing on collective experience from ten collaborative research projects focused on the Global South, we identify three major challenges that impede the translation of research on sustainability and resilience into better-informed choices by individuals and policy-makers that in turn can support transformation to a sustainable future. The three challenges comprise: (i) converting knowledge produced during research projects into successful knowledge application; (ii) scaling up knowledge in time when research projects are short-term and potential impacts are long-term; and (iii) scaling up knowledge across space, from local research sites to larger-scale or even global impact. Some potential pathways for funding agencies to overcome these challenges include providing targeted prolonged funding for dissemination and outreach, and facilitating collaboration and coordination across different sites, research teams, and partner organizations. By systematically documenting these challenges, we hope to pave the way for further innovations in the research cycle

Using click-chemistry for visualizing in situ changes of translational activity in planktonic marine bacteria

11 pages, 8 figures, supplementary material https://doi.org/10.3389/fmicb.2017.02360A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization. We also evaluated the use of this technique to track shifts in translational activity by comparing it with leucine incorporation, and used it to monitor temporal changes in both cultures and natural samples. Finally, we determined the optimal concentration and incubation time for substrate incorporation during BONCAT incubations at an oligotrophic site. Our results demonstrate that BONCAT is a fast and powerful semi-quantitative approach to explore the physiological status of marine bacteriaThis work was supported by grants EcoRARE (CTM2014-60467-JIN), funded by the Spanish Government and the European Regional Development Fund (ERDF), and REMEI (CTM2015-70340-R) funded by the Spanish GovernmentPeer Reviewe

Repeated drying and rewetting cycles accelerate bacterial growth recovery after rewetting

Two patterns of bacterial growth response upon drying and rewetting (DRW) of soils have previously been identified. Bacterial growth can either start increasing immediately after rewetting in a linear fashion (“type 1” response) or start increasing exponentially after a lag period (“type 2” response). The effect of repeated DRW cycles was studied in three soils with different response patterns after a single DRW cycle (“type 1”, “type 2” with a short lag period and “type 2” with a long lag period). The soils were exposed to seven DRW cycles, and respiration and bacterial growth were monitored after 1, 2, 3, 5, and 7 cycles. Exposure to repeated DRW shifted the bacterial growth response from a “type 2” to a “type 1” pattern, resulting in an accelerated growth recovery to a pre-disturbance growth rate. Bacterial growth in soils that initially had a “type 1” response also tended to recover faster after each subsequent DRW cycle. The respiration patterns after DRW also indicated the same transition from a “type 2” to a “type 1” pattern. Our results show that exposure to repeated DRW cycles will shape the bacterial response to future DRW cycles, which might be mediated by a shift in species composition, a physiological adjustment, evolutionary changes, or a combination of the three

Bacteria constrain the fungal growth response to drying-rewetting

Bacteria and fungi are the two principal decomposer groups in soils, determining rates of biogeochemical cycling. Rewetting of dry soils induces enormous dynamics in biogeochemistry. Bacteria have been shown to exhibit large variation in growth over time upon drying-rewetting (D/RW), however, in studies to date, fungal growth has shown limited responsiveness. Here we investigated whether fungal growth responses to D/RW are constrained by competition with bacteria by using the bactericide bronopol to suppress bacterial growth during D/RW. We examined responses for two different soils, previously shown to exhibit different bacterial growth responses to D/RW. Experimental elimination of bacterial growth lead to increased fungal growth in both soils upon D/RW, indicating a competitive release of fungal growth when bacteria were suppressed. We also observed a pronounced fungal growth response to D/RW for one of the soils, which has not been previously reported. In this case, even when rewetting with water (i.e. without bacterial suppression), fungal growth increased to reach rates 10-times greater than in the moist control soil. The peak in fungal growth coincided with a secondary peak of respiration, revealing a functional importance of fungi for C-cycling during D/RW. The decline in fungal growth following this peak also coincided with the onset of exponential bacterial growth, further strengthening evidence for a negative correlation between bacteria and fungi, suggesting that competition with bacteria can constrain the fungal growth response to D/RW

Drying intensity and acidity slow down microbial growth recovery after rewetting dry soils

Soil microbes perceive drying and rewetting (DRW) events as more or less harsh depending on the previous soil moisture history. If a DRW event is not perceived as harsh, microbial growth recovers rapidly after rewetting (referred to as ‘type 1’ response), while a harsh DRW will be followed by a delayed growth recovery (‘type 2’ response). Predicting these responses based on pedoclimatic factors is important because they can determine how carbon is partitioned between growth (soil C stabilization) and respiration (C loss to the atmosphere). To characterize the microbially perceived harshness between the two extreme types 1 and 2, and its pedoclimatic drivers, we described microbial growth with a single logistic function and respiration with a rescaled gamma distribution using ∼100 growth and respiration datasets. These functions captured microbial growth and respiration rates well during the recovery phase after rewetting. Therefore, the fitted parameters from these functions could help us to capture the continuum of microbial recovery between type 1 and 2 and characterize harshness levels. The product of growth parameters τ (delay time) and b (the slope of the growth curve at time τ) was an effective index that could capture and quantify perceived harshness because it allowed separating type 1 and 2 responses better than τ or b alone or than any other parameter describing the growth or respiration response. The drier the soil before rewetting and the lower the pH, the higher was the perceived harshness (τ×b), the longer the delay of growth recovery, and the larger the CO2 loss at rewetting. Overall, this study places soil microbial responses to DRW along a continuous gradient from fast to slow recovery, where the faster the recovery, the better adapted the microbial community is to the DRW event