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Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015–2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH,nrfA,aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

 

ABSTRACT The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides , Dehalogenimonas , and “ Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.e., not impacted with organohalogens of anthropogenic origin). The broad environmental distribution of Dehalococcoidia , as well as other organohalide-respiring bacteria, supports the concept of active halogen cycling and the natural formation of organohalogens in various ecosystems. Dechlorination reduces recalcitrance and renders organics susceptible to metabolic oxidation by diverse microbial taxa. During reductive dechlorination, hydrogenotrophic organohalide-respiring bacteria, in particular Dehalococcoidia , can consume hydrogen to low consumption threshold concentrations (<0.3 nM) and enable syntrophic oxidation processes. These functional attributes and the broad distribution imply that Dehalococcoidia play relevant roles in carbon cycling in anoxic ecosystems. 

To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO₃⁻g⁻¹dry soil d⁻¹) and accumulation of N₂O after 192 hours of incubation. Nitrification activity (NH₄⁺ → NH₂OH → NO → NO₂^- → NO₃⁻) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

 

Nonnative conifers are widespread in the southern hemisphere, where their use as plantation species has led to adverse ecosystem impacts sometimes intensified by invasion. Mechanical removal is a common strategy used to reduce or eliminate the negative impacts of nonnative conifers, and encourage native regeneration. However, a variety of factors may preclude active ecological restoration following removal. As a result, passive restoration – unassisted natural vegetation regeneration – is common following conifer removal. We asked, ‘what is the response of understorey cover to removal of nonnative conifer stands followed by passive restoration?' We sampled understorey cover in three site types: two‐ to ten‐year‐old clearcuts, native forest and current plantations. We then grouped understorey species by origin (native/nonnative) and growth form, and compared proportion and per cent cover of these groups as well as of bare ground and litter between the three site types. For clearcuts, we also analysed the effect of time since clearcut on the studied variables. We found that clearcuts had a significantly higher average proportion of nonnative understorey vegetation cover than native forest sites, where nonnative vegetation was nearly absent. The understorey of clearcut sites also averaged more overall vegetation cover and more nonnative vegetation cover (in particular nonnative shrubs and herbaceous species) than either plantation or native forest sites. Notably, 99% of nonnative shrub cover in clearcuts was the invasive nonnative species Scotch broom (Cytisus scoparius). After ten years of passive recovery since clearcutting, the proportion of understorey vegetation cover that is native has not increased and remains far below the proportion observed in native forest sites. Reduced natural regeneration capacity of the native ecosystem, presence of invasive species in the surrounding landscape and land‐use legacies from plantation forestry may inhibit native vegetation recovery and benefit opportunistic invasives, limiting the effectiveness of passive restoration in this context.

Abstract in Spanish is available with online material.