The Saltpan Microbiome is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication

As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to model the combined stresses of saltwater intrusion and coastal eutrophication. Initially, sediment prokaryotic composition was similar to prior studies of freshwater marsh but diverged over time, reflecting the magnitude of increase in saltwater. There was no observed effect of nutrient amendment, potentially ranking seawater intrusion as a higher-importance compositional driver. Although the previously described loss of methanogenic populations and promotion of sulfate reducers in response to saltwater exposure was observed, taxonomic distribution was not similar to typical meso-polyhaline wetlands. Without colonization by marine taxa, such a community may be short-lived naturally, ultimately equilibrating with more common saltmarsh species. However, the recapitulation of salinity concentration by freshwater sediment microbial composition demonstrates the overwhelming nature of saltwater intrusion relative to other drivers like eutrophication.

Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert

The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.

Taxonomic Characterization, Antiviral Activity and Induction of Three New Kenalactams in Nocardiopsis sp. CG3

Exploration of secondary metabolites secreted by new Actinobacteria taxa isolated from unexplored areas, can increase the possibility to obtain new compounds which can be developed into new drugs for the treatment of serious diseases such as hepatitis C. In this context, one actinobacterial strain, CG3, has been selected based on the results of polyphasic characterization, which indicate that it represents a new putative species within the genus Nocardiopsis. Two fractions (F2 and F3), prepared from the culture of strain CG3 in soybean medium, exhibited a pronounced antiviral activity against the HCV strain Luc-Jc1. LC–HRESIMS analysis showed different bioactive compounds in both active fractions (F2 and F3), including five polyenic macrolactams (kenalactams A-E), three isoflavone metabolites, along with mitomycin C and one p-phenyl derivative. Furthermore, feeding with 1% of methionine, lysine or alanine as a unique nitrogen source, induced the production of three novel kenalactam derivatives.

Microbial Communities in Saltpan Sediments Show Tolerance to Mars Analog Conditions, but Susceptibility to Chloride and Perchlorate Toxicity

Brines at or near the surface of present-day Mars are a potential explanation for seasonally recurring dark streaks on the walls of craters, termed recurring slope lineae (RSL). Deliquescence and freezing point depression are possible drivers of brine stability, attributable to the high salinity observed in martian regolith including chlorides and perchlorates. Investigation of life, which may inhabit RSL, and the cellular mechanisms necessary for survival, must consider the tolerance of highly variable hydration, freeze-thaw cycles, and high osmolarity in addition to the anaerobic, oligotrophic, and irradiated environment. We propose the saltpan, an ephemeral, hypersaline wetland as an analogue for putative RSL hydrology. Saltpan sediment archaeal and bacterial communities showed tolerance of the Mars-analogous atmosphere, hydration, minerology, salinity, and temperature. Although active growth and a shift to well-adapted taxa were observed, susceptibility to low-concentration chloride and perchlorate addition suggested that such a composition was insufficient for beneficial water retention relative to added salt stress.

Microorganisms that participate in biochemical cycles in wetlands

Several biochemical cycles are performed in natural wetlands (NWs) and constructed wetlands (CWs). The knowledge of the microorganisms could be used to monitor the restoration of wetlands or the performance of the wastewater treatment. Regarding bacteria, Proteobacteria phylum is the most abundant in NWs and CWs, which possesses a role in N, P, and S cycles, and in the degradation of organic matter. Other phyla are present in lower abundance. Archaea participate in methanogenesis, methane oxidation, and the methanogenic N2 fixation. Sulfur and phosphorus cycles are also performed by other microorganisms, such as Chloroflexi or Nitrospirae phyla. In general, there is more information about the N cycle, especially nitrification and denitrification. Processes where archaea participate (e.g. methane oxidation, methanogenic N2 fixation) are still unclear their metabolic role and several of these microorganisms have not been isolated so far. The study can use 16S rDNA genes or functional genes. The use of functional genes gives information to monitor specific microbial populations and 16S rDNA is more suitable to perform the taxonomic classification. Also, there are several Candidatus microorganisms, which have not been isolated so far. However, it has been described their metabolic role in the biochemical cycles in wetlands.

Investigation of the antimony fractions and indigenous microbiota in aerobic and anaerobic rice paddies

The accumulation of antimony (Sb) by rice is a severe threat to exposed populations. Previous studies demonstrated that, compared to flooded (anaerobic) water management, dry cultivation management (aerobic) could substantially decrease As, an analog of Sb, uptake by rice. However, the effects of different water management strategies on the accumulation of Sb by rice are less understood. It is proposed that microorganisms play an important role in regulating Sb mobility in rice paddies. Hence, the current study compared the microbial communities in rice paddies receiving different water management, i.e., flooded (anaerobic) and dry (aerobic)) rice cultivation. Significant decrease in Sb uptake by rice, in both the roots and grains, was observed under the aerobic compared to the anaerobic conditions. This could partially be attributed to the differences in the microbial communities as shaped by the redox environment. In aerobic soils, the gene responsible for Sb oxidation (i.e., aioA) was significantly, while in anaerobic soils the gene responsible for Sb reduction (i.e., arrA) was enriched, suggesting that variation in redox conditions may trigger different microbial responses. Accordingly, geochemical analysis indicated that accumulation of Sb(III) was only observed under anaerobic conditions, but not under aerobic conditions. The environment-microbe interactions were distinct between the two treatments with a greater number of interactions between Sb fractions and the microbial assemblage under anaerobic conditions, while Eh was the most influential geochemical parameter under aerobic conditions. Finally, the presence of a core microbiome under the two conditions suggested the possibility of microorganisms that support rice growth, nutrition, and health. The reduction of Sb in rice grain significantly decreases Sb exposure to the residents in Sb contaminated regions, and should be considered for future rice cultivation practices.