Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils

Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation

The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions

Impacts of chemical dispersants on oil-degrading microorganisms

Dissertation ist gesperrt bis 01.01.2023 !Die ökologischen Folgen von Erdöleinträgen in die Weltmeere sind oft verheerend. Zu den möglichen Bekämpfungsmaßnahmen gehört auch der Einsatz von chemischen Dispersionsmitteln (Mischungen aus Tensiden und Lösungsmitteln), die Ölteppiche und Ölansammlungen an den Küsten reduzieren sollen. Allerdings ist ihr Einsatz umstritten, da diese Mittel selbst toxisch sein können und ihre ökologischen Effekte noch nicht komplett erforscht sind. Besonders große Wissenslücken existieren bezüglich ihrer Effekte auf die mikrobiellen Gemeinschaften im Meerwasser und die Öl abbauenden Bakterien. Die wissenschaftliche Literatur zu diesem Thema beinhaltet viele (größtenteils unerklärte) widersprüchliche Ergebnisse und kaum Daten dazu, welche zellulären Mechanismen den beobachteten Effekten von chemischen Dispersionsmitteln auf Kohlenwasserstoff abbauende Bakterien zu Grunde liegen. Deshalb war das Ziel dieser Doktorarbeit, die Auswirkungen von chemischen Dispersionsmitteln auf Öl abbauende Mikroorganismen zu ermitteln und auf verschiedenen ökologischen Ebenen zu untersuchen. Zunächst wurde die Reaktion von mikrobiellen Meerwassergemeinschaften aus dem Arktischen Ozean und der Nordsee auf den Kontakt mit einem chemischen Dispersionsmittel (Corexit EC9500A) während eines simulierten in Mikrokosmenexperimenten untersucht. Während der Abbau von Alkanen und kleinen aromatischen Kohlenwasserstoffen nicht wirklich von den chemischen Dispersionsmitteln beeinträchtigt wurde, wurden dennoch niedrigere Zellzahlen und die Entstehung einer anderen mikrobiellen Gemeinschaft aus Kohlenwasserstoff und/oder Dispersionsmittel abbauenden Bakterien beobachtet. Zudem wurden persistente organische Stoffe (vermutlich Lösungsmittel aus dem Dispersionsmitel) in Mikrokosmen mit zugegebenem Dispersionsmittel detektiert und die Zugabe von Nährstoffen (Biostimulation) als ein vielversprechender alternativer Ansatz im Kontext von potentiellen künftigen Ölunfällen im Arktischen Ozean identifiziert. Anschließend wurde der marine Modellorganismus Marinobacter sp. TT1 untersucht, um die Auswirkungen von chemischen Dispersionsmitteln auf das Wachstum, den Alkanabbau und verschiedene zelluläre Prozesse dieses Organismus zu bestimmen. Es zeigte sich, dass das Wachstum und der Alkanabbau einer vorher hungernden Kultur von Marinobacter sp. TT1 nach Zugabe von Corexit signifikant gehemmt wurden. Diese Ergebnisse demontrierten zum ersten Mal, dass Substratlimitierung, welche die Bedingungen im oligotrophen offenen Ozean widerspiegelt, die Reaktion von Kohlenwasserstoff abbauenden Bakterien auf Corexit beeinflussen kann. Eine vergleichende Proteomanalyse des Modellorganismus unter verschiedenen Kultur- und Substratbedingungen ergab außerdem, dass durch Corexit verursachte Änderungen im Proteom vor allem mit dem Metabolismus von Kohlenwasserstoffen, chemotaktischer Motilität, der Bildung von Aggregaten/Biofilmen und Toleranzmechanismen gegenüber Lösungsmitteln in Verbindung standen. Weiterhin konnten zum ersten Mal Proteine identifiziert werden, welche mit einem vermuteten mikrobiellen Abbau von Corexitbestandteilen zusammenhängen und die ersten Hinweise auf Alginatbiosynthese in einem Marinobacter spp. im Zusammenhang des Hexadekanabbaus dokumentiert werden. Zusammen betrachtet vertiefen die präsentierten Erkenntnisse unser Verständnis davon wie und warum chemische Dispersionsmittel Auswirkungen auf Öl abbauende Mikroorganismen haben. Die Anwendung von Dispersionsmitteln im Meer hat vermutlich in den meisten Fällen ausgeprägte Effekte auf marine Mikrobengemeinschaften und verändert deren Zusammensetzung, indem bestimmte Kohlenwasserstoff oder Dispersionsmittel abbauende mikrobielle Gruppen bevorzugt angereichert und andere Gruppen gehemmt werden. Darüber hinaus wurden im Rahmen dieser Doktorarbeit mehrere mögliche Erklärungen für die inkonsistente Literaturlage zur Frage der Auswirkungen von chemischen Dispersionsmitteln auf Öl abbauende Mikroorganismen gefunden. Die in dieser Doktorarbeit erzielten neuen Einblicke könnten weitreichende ökologische Konsequenzen haben und sollten während zukünftiger Planung von Ölunfall-Bekämpfungsmaßnahmen berücksichtigt werden.Accidental crude oil spills can cause substantial environmental damage in marine ecosystems. During the emergency spill response, chemical dispersants (= solvent-surfactant mixtures) are often applied with the aim of reducing ecological and economic damage due to floating and beached oil. However, the use of chemical dispersants remains controversial due to their inherent toxicity potential and uncertainties about their ecological effects, including their influence on affected seawater microbial communities and native oil/hydrocarbon-degrading microorganisms. The scientific literature on this topic is characterized by contradictory findings and a lack of data on the underlying mechanisms of observed dispersant effects on oil-degrading bacteria. Therefore, this work aimed to determine and elucidate the impacts of chemical dispersants on oil-degrading microorganisms by examining their effects on different ecological levels. First, the response of environmental seawater microbial communities from the Arctic Ocean and the North Sea to chemical dispersant exposure was determined by performing laboratory seawater microcosm experiments that simulated oil spill conditions and monitored oil biodegradation potential, as well as microbial community dynamics. These studies showed that while biodegradation of several aliphatic and aromatic hydrocarbons was not substantially affected by chemical dispersant addition, lower cell numbers and the enrichment of a distinct community of hydrocarbon- and/or dispersant-degrading bacterial taxa were observed. Additionally, persistent organic compounds (likely dispersant-derived) were observed in dispersant-amended microcosms and the application of inorganic nutrients (i.e. biostimulation) was identified as a promising alternative approach to dispersant application in potential future Arctic Ocean oil spills. Next, the model organism Marinobacter sp. TT1 was investigated in order to identify the effects of chemical dispersant exposure on growth, alkane biodegradation activity and cellular processes of this marine hydrocarbon degrader. The growth and n hexadecane biodegradation efficiency of previously starved cells was significantly inhibited when exposed to the dispersant, revealing that substrate limitation, resembling oligotrophic open ocean conditions, can affect the microbial response to dispersants. Comparative proteomic analyses indicated that the chemical dispersant Corexit EC9500 affected hydrocarbon metabolism, chemotactic motility, and biofilm formation, while also inducing solvent-stress response mechanisms in Marinobacter sp. TT1. For the first time, the proteins associated with a proposed microbial metabolism of Corexit components as carbon substrates were identified, revealing that strain TT1 likely metabolized different components of Corexit EC 9500. Furthermore, the first evidence of alginate biosynthesis associated with the metabolism of n-hexadecane in a member of the Marinobacter genus was also documented. Taken together, the obtained findings significantly deepen our understanding of how and why chemical dispersants impact oil-degrading microorganisms and should be taken into consideration during future oil spill response planning

Photophysiological response of Symbiodiniaceae single cells to temperature stress

Photosynthetic dinoflagellates in the family Symbiodiniaceae engage in symbiosis with scleractinian corals. As coral ‘bleaching’ is partly governed by the thermal sensitivity of different Symbiodiniaceae lineages, numerous studies have investigated their temperature sensitivity. However, the systematic identification of single-cells with increased temperature resistance among these dinoflagellates has remained inaccessible, mostly due to a lack of technologies operating at the microscale. Here, we employed a unique combination of microfluidics, miniaturized temperature control, and chlorophyll fluorometry to characterize the single-cell heterogeneity among five representative species within the Symbiodiniaceae family under temperature stress. We monitored single-cell maximum quantum yields (Fv/Fm) of photosystem (PS) II under increasing temperature stress (22‒39 °C, + 1 °C every 15 min), and detected a significant Fv/Fm reduction at lineage-specific temperatures ranging from 28 °C to 34 °C alongside a 40- to 180- fold increase in intraspecific heterogeneity under elevated temperatures (&gt;31 °C). We discovered that the initial Fv/Fm of a cell could predict the same cell’s ability to perform PSII photochemistry under moderate temperature stress (&lt;32 °C), suggesting its use as a proxy for measuring the thermal sensitivity among Symbiodiniaceae. In combination, our study highlights the heterogeneous thermal sensitivity among photosynthetic Symbiodiniaceae and adds critical resolution to our understanding of temperature-induced coral bleaching