Carotenoid biomarkers in Namibian shelf sediments: Anoxygenic photosynthesis during sulfide eruptions in the Benguela Upwelling System.

Aromatic carotenoid-derived hydrocarbon biomarkers are ubiquitous in ancient sediments and oils and are typically attributed to anoxygenic phototrophic green sulfur bacteria (GSB) and purple sulfur bacteria (PSB). These biomarkers serve as proxies for the environmental growth requirements of PSB and GSB, namely euxinic waters extending into the photic zone. Until now, prevailing models for environments supporting anoxygenic phototrophs include microbial mats, restricted basins and fjords with deep chemoclines, and meromictic lakes with shallow chemoclines. However, carotenoids have been reported in ancient open marine settings for which there currently are no known modern analogs that host GSB and PSB. The Benguela Upwelling System offshore Namibia, known for exceptionally high primary productivity, is prone to recurrent toxic gas eruptions whereupon hydrogen sulfide emanates from sediments into the overlying water column. These events, visible in satellite imagery as water masses clouded with elemental sulfur, suggest that the Benguela Upwelling System may be capable of supporting GSB and PSB. Here, we compare distributions of biomarkers in the free and sulfur-bound organic matter of Namibian shelf sediments. Numerous compounds-including acyclic isoprenoids, steranes, triterpanes, and carotenoids-were released from the polar lipid fractions upon Raney nickel desulfurization. The prevalence of isorenieratane and ß-isorenieratane in sampling stations along the shelf verified anoxygenic photosynthesis by low-light-adapted, brown-colored GSB in this open marine setting. Renierapurpurane was also present in the sulfur-bound carotenoids and was typically accompanied by lower abundances of renieratane and ß-renierapurpurane, thereby identifying cyanobacteria as an additional aromatic carotenoid source.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf.

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth's climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

The assembly of the Cape flora is consistent with an edaphic rather than climatic filter.

The Cape flora is compositionally biased, being dominated by a few fynbos clades (such as Iridaceae, Ericaceae, Proteaceae and Restionaceae) that make up major part of the distinct heathland vegetation in the Cape Floristic Region. Uncertainty exists concerning what excluded the subtropical to tropical palm-dominated woodland/forest vegetation that was the dominant component in the CFR in the Paleocene and allowed the fynbos clades, which are largely derived from outside Africa, to establish and radiate. Two filters have been proposed. The first postulates that the establishment of the Mediterranean climate driven by the late Miocene initiation of the cold-water Benguela Upwelling System (BUS) eliminated the African lineages and allowed the establishment and radiation of sclerophyllous plant clades ("the Mediterranean climate model", MCM). Alternatively, the "oligotrophic soils model" (OSM) postulates that the oligotrophic soils, gradually exhumed by post-Gondwanan Late Cretaceous - early Cenozoic erosion, acted as a filter excluding the African lineages. In this study, we re-calibrate the fynbos clade Phylica (Rhamnaceae), the genus initially used to test the MCM, using new fossil data to test if the crown age precedes the Late Miocene. Our results indicate that we cannot significantly reject a crown age of Phylica consistent with the MCM. We compare the MCM and OSM model for the Cape fynbos flora by compiling the crown ages of 22 fynbos clades. We show that crown ages are not clustered in time around the initiation of the BUS but, are dispersed throughout the Cenozoic. This suggests that oligotrophic soils, rather than summer drought, acted as a filter. Consequently, we argue that the fynbos clades radiated separately in expanding edaphically controlled heathland patches in the Cape mountains as sandstone exhumation after the Gondwanan break-up progressed.

Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia.

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.

Tracing the upwelling process in the northern Benguela upwelling system (nBUS) by 129I.

New data on the presence of 129I in seawater in the Southern Hemisphere measured by Accelerator Mass Spectrometry (AMS) is presented. The samples were collected in 2014 along the Namibian coast during a cruise organised by the National Marine Information and Research Centre (NatMIRC), the national laboratories of the Ministry of Fisheries and Marine Resources (MFMR) in Namibia, and the IAEA Environment Laboratories (IAEA NAEL) in Monaco. The Benguela upwelling system is known as one of the most important marine upwelling regions in the world. Strong winds induce an offshore transport of surface seawater which is substituted by cool subsurface water inshore. As this water is nutrient-rich, which leads to high primary productivity, the Benguela upwelling system has a very important role as a fishing production area. The 129I concentrations in samples were between (0.66 ± 0.14) × 107 and (1.45 ± 0.30) × 107 atoms/kg. The highest 129I concentrations were found in the offshore surface samples. Deep-sea and inshore samples contained lower 129I concentrations, possibly as an effect of the upwelling process. A comparison with previously published studies suggests that the presence of 129I in the northern Benguela upwelling system (nBUS), is mainly due to the impact of nuclear weapons global fallout, without any evident impact of nuclear fuel reprocessing.

Harmful algal blooms of the Benguela eastern boundary upwelling system.

The Benguela Upwelling System (BUS) is subject to a high incidence of HABs. Of the major shellfish poisoning syndromes associated with HABs, Paralytic and Diarrhetic Shellfish Poisoning (PSP and DSP) pose the greatest concern, but as documented herein there are several other HAB organisms that are also present. Blooms of Alexandrium catenella have been recognised as the typical cause of PSP since 1948. In addition to the risk posed to human health A. catenella has also been the cause of large shellfish and bird mortalities. An additional risk of PSP is provided by Alexandrium minutum first detected in Cape Town harbour in 2003. DSP was identified on the South African coast for the first time in 1991. Although several Dinophysis spp. known to cause DSP have been recognized as a component of the plankton of the region, it is accepted that DSP is usually attributed to D. acuminata or D. fortii. In the southern Benguela both Pseudo-nitzschia australis and Pseudo-nitzschia multiseries have been identified and shown to produce domoic acid. Multiple Pseudo-nitzschia spp. have been identified in the northern Benguela with the potentially toxigenic Pseudo-nitzschia pungens and P. australis dominant inshore. The yessotoxin (YTX) producing dinoflagellates Gonyaulax spinifera, Lingulodinium polyedrum and Protoceratium reticulatum are all known to form blooms and YTXs have been the cause of massive mortalities of farmed abalone. Prominent fish-killing blooms include Karlodinium veneficum in the northern Benguela and Karenia cristata in the southern Benguela. Shellfish farms in an embayment of the southern Benguela have suffered reduced growth rates due to the ecosystem disruptive blooms of Aureococcus anophagefferens. High biomass dinoflagellate blooms often attributed to Tripos and Prorocentrum spp. characterise the entire region and major mortalities of marine life are regularly attributed to their decay and the subsequent development of anoxic conditions.

Morphology and toxicity of Pseudo-nitzschia species in the northern Benguela Upwelling System.

The Benguela upwelling system, considered the world's most productive marine ecosystem, has a long record of potentially toxic diatoms belonging to the genus Pseudo-nitzschia. Species of Pseudo-nitzschia were reported as early as 1936 from the northern Benguela upwelling system (nBUS). For the current study, long-term phytoplankton monitoring data (2004-2011) for the Namibian coast were analysed to examine inshore and offshore temporal distribution of Pseudo-nitzschia species, their diversity and ultrastructure. The potentially toxigenic P. pungens and P. australis were the dominant inshore species, whereas offshore Pseudo-nitzschia showed a higher diversity that also included potentially toxic species. During a warming event, a community shift from P. pungens and P. australis dominance to P. fraudulenta and P. multiseries was documented in the central nBUS. A case study of a toxic event (August 2004) revealed that P. australis and P. pungens were present at multiple inshore and offshore stations, coincident with fish (pilchard) and bird mortalities reported from the central part of Namibia. Toxin analyses (LC-MS/MS) of samples collected from June to August 2004 revealed the presence of particulate domoic acid (DA) in seawater at multiple stations (maximum ∼180 ng DA/L) in the >0.45 µm size-fraction, as well as detectable DA (0.12 µg DA/g) in the gut of one of two pilchard samples tested. These findings indicate that DA may have been associated with the fish and bird mortalities reported from this event in the nBUS. However, the co-occurrence of very high biomass phytoplankton blooms suggests that other explanations may be possible.