Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

Abstract

Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

“…Temporally, the diel patterns of trophic interactions (orchestrated by phototrophs) drive the shift in activity distribution of microbial activity as has been shown from Namib Desert soil (Gunnigle et al, 2017). Spatially, these complex trophic interactions take place within thin biocrusts and yield emergent spatial distributions of microbial groups as depicted in Fig.…”

Microbial Community Responses to Modern Environmental and Past Climatic Conditions in Omongwa Pan, Western Kalahari: A Paired 16S rRNA Gene Profiling and Lipid Biomarker Approach

“…The most frequently found orders were Rhizobiales, Burkhoderiales, Methylophilales , and Pseudomonadales. Proteobacteria were often found in desert soil bacterial communities (Gunnigle et al, ; Lefevre et al, ; Spain et al, ) and may be functionally relevant in nutrient‐limited arid environments (Boldareva‐Nuianzina et al, ). We can summarize that near‐surface layers of Omongwa pan are an important habitat for dry‐adapted and halophilic bacteria as well as halophilic archaea.…”

“…The organisms are known to increase soil fertility (providing nutrients) and soil moisture retention (Pointing & Belnap, 2012) and thus influence the germination, survival, and nutritional status of the widely spaced vascular plants (Makhalanyane et al, 2015). Actinobacteria had been described as a dominant phylum in arid environments, such as the Namib Desert (Gunnigle et al, 2017;Makhalanyane et al, 2013). In Omongwa pan thermotolerant Actinomycetales (Kurapova et al, 2012) occured sporadically in C1 and C2.…”

Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a dessicated Namib Desert soil

“…According to current models, aridity results in habitat fragmentation, both geographically leading to “islands” of microbial biomass and diversity and temporally, producing long periods of functional inactivity (Pointing and Belnap, 2012; Collins et al , 2014). However, recent evidence suggests that some activity is retained under these extreme conditions (Gunnigle et al , 2017; Schulze-Makuch et al , 2018). In recent years, the microbial ecology of various Namib Desert edaphic niches has been extensively studied (e.g.…”

“…The short life-span and high turnover of messenger RNA (Belasco and Brawerman, 1993) allows ephemeral states of microbial communities to be captured without significant interference from legacy biomolecules or inactive microbial populations, as might be the case in DNA- or protein-based studies (Nielsen et al , 2006). In desert environments, active community changes over diel cycles or after rainfall have been described by 16S rRNA amplicon transcriptome studies (Gunnigle et al , 2017; Štovíček et al , 2017).…”