Lipid biomarker signatures as tracers for harmful cyanobacterial blooms in the Baltic Sea

Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach

The eastern Arabian Sea (EAS) is known for its unique oceanographic features such as the seasonal monsoonal winds, upwelling of nutrient-rich waters and a significant increase in primary productivity during the monsoon season. In this study, we utilised the shotgun metagenomics approach to determine the seasonal variations in bacterial taxonomic and functional profiles during the non-monsoon and monsoon seasons in the EAS. Significant seasonal variations in the bacterial community structure were observed at the phylum and genera levels. These findings also correspond with seasonal shifts in the functional profiles of the bacterial communities based on the variations of genes encoding enzymes associated with different metabolic pathways. Pronounced seasonal variation of bacterial taxa was evident with an increased abundance of Idiomarina, Marinobacter, Psychrobacter and Alteromonas of Proteobacteria, Bacillus and Staphylococcus of Firmicutes during the non-monsoon season. These taxa were linked to elevated nucleotide and amino acid biosynthesis, amino acid and lipid degradation. Conversely, during the monsoon, the taxa composition changed with Alteromonas, Candidatus Pelagibacter of Proteobacteria and Cyanobacteria Synechococcus; contributing largely to the amino acid and lipid biosynthesis, fermentation and inorganic nutrient metabolism which was evident from functional analysis. Regression analysis confirmed that increased seasonal primary productivity significantly influenced the abundance of genes associated with carbohydrate, protein and lipid metabolism. These highlight the pivotal role of seasonal changes in primary productivity in shaping the bacterial communities, their functional profiles and driving the biogeochemical cycling in the EAS.

Developing a genetic approach to target cyanobacterial producers of heterocyte glycolipids in the environment

Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be used to detect the presence of heterocytous cyanobacteria in present-day and past environments, providing insight into the functioning of the studied ecosystems. However, due to their good preservation throughout time, heterocyte glycolipids are not ideal to detect and study living communities, instead methods based on DNA are preferred. Currently cyanobacteria can be detected using untargeted genomic approaches such as metagenomics, or they can be specifically targeted by, for example, the use of primers that preferentially amplify their 16S rRNA gene or their nifH gene in the case of nitrogen fixing cyanobacteria. However, since not all cyanobacterial nitrogen fixers are heterocytous, there is currently no fast gene-based method to specifically detect and distinguish heterocytous cyanobacteria. Here, we developed a PCR-based method to specifically detect heterocytous cyanobacteria by designing primers targeting the gene (hglT) encoding the enzyme responsible for the last step in the biosynthesis of heterocyte glycolipid (i.e., a glycosyltransferase). We designed several primer sets using the publicly available sequences of 23 heterocytous cyanobacteria, after testing them on DNA extracts of 21 heterocyte-forming and 7 non-heterocyte forming freshwater cyanobacteria. The best primer set was chosen and successfully used to confirm the presence of heterocytous cyanobacteria in a marine environmental sample.

Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA

Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.

Change of the structure and assembly of bacterial and photosynthetic communities by the ecological engineering practices in Dianchi Lake

Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is an eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physicochemical variables and aquatic microbial communities. Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p < 0.05). Redundancy analysis and microbial ecological network suggested that microbial communities in Caohai had a higher stability. Deterministic process dominated the microbial assembly (50-80% for bacteria and >90% for photoautotrophs), and particularly in Caohai. Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects.

Lipid Biomarkers From Microbial Mats on the McMurdo Ice Shelf, Antarctica: Signatures for Life in the Cryosphere

Persistent cold temperatures, a paucity of nutrients, freeze-thaw cycles, and the strongly seasonal light regime make Antarctica one of Earth's least hospitable surface environments for complex life. Cyanobacteria, however, are well-adapted to such conditions and are often the dominant primary producers in Antarctic inland water environments. In particular, the network of meltwater ponds on the 'dirty ice' of the McMurdo Ice Shelf is an ecosystem with extensive cyanobacteria-dominated microbial mat accumulations. This study investigated intact polar lipids (IPLs), heterocyte glycolipids (HGs), and bacteriohopanepolyols (BHPs) in combination with 16S and 18S rRNA gene diversity in microbial mats of twelve ponds in this unique polar ecosystem. To constrain the effects of nutrient availability, temperature and freeze-thaw cycles on the lipid membrane composition, lipids were compared to stromatolite-forming cyanobacterial mats from ice-covered lakes in the McMurdo Dry Valleys as well as from (sub)tropical regions and hot springs. The 16S rRNA gene compositions of the McMurdo Ice Shelf mats confirm the dominance of Cyanobacteria and Proteobacteria while the 18S rRNA gene composition indicates the presence of Ochrophyta, Chlorophyta, Ciliophora, and other microfauna. IPL analyses revealed a predominantly bacterial community in the meltwater ponds, with archaeal lipids being barely detectable. IPLs are dominated by glycolipids and phospholipids, followed by aminolipids. The high abundance of sugar-bound lipids accords with a predominance of cyanobacterial primary producers. The phosphate-limited samples from the (sub)tropical, hot spring, and Lake Vanda sites revealed a higher abundance of aminolipids compared to those of the nitrogen-limited meltwater ponds, affirming the direct affects that N and P availability have on IPL compositions. The high abundance of polyunsaturated IPLs in the Antarctic microbial mats suggests that these lipids provide an important mechanism to maintain membrane fluidity in cold environments. High abundances of HG keto-ols and HG keto-diols, produced by heterocytous cyanobacteria, further support these findings and reveal a unique distribution compared to those from warmer climates.

Vitamin B12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification

Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B₁₂) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.

A geophysical, geochemical and microbiological study of a newly discovered pockmark with active gas seepage and submarine groundwater discharge (MET1-BH, central Gulf of Gdańsk, southern Baltic Sea)

High-resolution bathymetric data were collected with a multi-beam echosounder in the southern part of the Baltic Sea (region MET1, Gulf of Gdańsk) revealing the presence of a 10 m deep and 50 m in diameter pockmark (MET1-BH) on the sea bottom (78.7 m). To date, no such structures have been observed to reach this size in the Baltic Sea. The salinity of the near-bottom water in the pockmark was about 2 PSU (about 31.22 mmol/l Cl^-), which clearly indicated the presence of a submarine groundwater discharge (SGD). Water column, sediments and the seabed structure were investigated in the MET1-BH area using various hydroacoustic devices: multi-beam and splitbeam echosounders and a sub-bottom profiler. Geochemical analyses of sediment pore waters (CH₄, Cl^-, Br^-, F^-, SO₄^2-, Ca²⁺, Mg²⁺, K⁺, Na⁺, ∑H₂S, dP, dSi, NH₄⁺, DIC, DOC) and microbiological analysis of sediments (16S rRNA) were performed. The content of CH₄ and CO₂ in the outflowing gas and its origin (δ¹³C-CH₄ and δ²D-CH₄) were determined. Hydroacoustic data showed that gas was emitted intensively from the inside of the structure. The height and intensity of the gas flares varied depending on the hydrostatic pressure. The gas contained 76.1% of CH₄, 17.6% of CO₂ and 0.39% of He. Methane source was microbial. Geophysical investigation revealed the presence of dislocations in sub-surface sediment layers in the MET1 region, which could have created a passage for groundwater and gas. Geochemical analyses pointed to intensive processes of organic matter decomposition in this area, active methanogenesis in the surface sediment layer, lack of the sulphate-methane transition, and freshwater seepage at a depth of ~88 m (bottom of the pockmark), probably from Upper Cretaceous deposits. The Prokaryota composition, atypical for marine surface sediments, resulted from the combination of freshwater and high organic matter content, and reflected active in situ methanogensis.

Zooplankton impact on lipid biomarkers in water column vs. surface sediments of the stratified Eastern Gotland Basin (Central Baltic Sea)

Sediments from stratified marine environments often show an enhanced preservation of organic matter (OM) which is attributed to the limitation, or absence, of oxygen in the bottom waters and surface sediments. Yet there is still a limited knowledge about the changes that the associated biomarker signals undergo in the different parts of a stratified environment, and as to which extent the situation in the productive upper parts of the water column is eventually reflected in the sedimentary record. To better understand these processes we studied particulate matter samples from the stratified, partly anoxic Eastern Gotland Basin (EGB, Central Baltic Sea) during a strong cyanobacterial bloom in August 2016. Endmember samples representing the main biomass producers within the phytoplankton (cyanobacteria) and mesozooplankton (copepods) were obtained from different levels of the water column. Major extractable lipids (fatty acids, n-alcohols, sterols, and selected hydrocarbons) were analysed from the same materials and compared to samples cored from the underlying surface sediments (0-12 cm). Given the annually recurring phenomenon of cyanobacterial blooms we anticipated to find a considerable lipid footprint of the major primary producers in the sedimentary record of the EGB. Unexpectedly, however, lipids in the surface sediments largely derived from the storage lipids (mainly wax esters) of the copepod Pseudocalanus spp. which thrived in deeper, more saline and oxygen-depleted waters. Carbon number and unsaturation patterns suggest that the component n-alcohols of these wax esters are transformed into the corresponding n-fatty acids prior to further degradation in the sediment. In the EGB deposits, most of the plankton-derived lipids studied appear to be degraded on a time scale of decades. In terms of relative abundances, long-chain n-alkyl lipids and C29 sterols from terrestrial plant sources instead become predominant in the deeper sediment layers. Likewise, higher stanol/sterol ratios of C27-sterols vs. C29-sterols indicate a more intense biodegradation of planktonic OM as compared to terrestrial OM. Our observations indicate that primary produced particulate OM is heavily modified by mesozooplankton grazing. This overprint adds on the influence of heterotrophic microorganisms and, in the sediment, preferential preservation of terrestrial biomarkers. Taken together, these factors result in a major decoupling of the biomarker signals between the productive upper mixed layer and the oxygen-depleted bottom waters and sediments of the EGB.

Temperate rainforests near the South Pole during peak Cretaceous warmth

The mid-Cretaceous period was one of the warmest intervals of the past 140 million years^1-5, driven by atmospheric carbon dioxide levels of around 1,000 parts per million by volume⁶. In the near absence of proximal geological records from south of the Antarctic Circle, it is disputed whether polar ice could exist under such environmental conditions. Here we use a sedimentary sequence recovered from the West Antarctic shelf-the southernmost Cretaceous record reported so far-and show that a temperate lowland rainforest environment existed at a palaeolatitude of about 82° S during the Turonian-Santonian age (92 to 83 million years ago). This record contains an intact 3-metre-long network of in situ fossil roots embedded in a mudstone matrix containing diverse pollen and spores. A climate model simulation shows that the reconstructed temperate climate at this high latitude requires a combination of both atmospheric carbon dioxide concentrations of 1,120-1,680 parts per million by volume and a vegetated land surface without major Antarctic glaciation, highlighting the important cooling effect exerted by ice albedo under high levels of atmospheric carbon dioxide.

Cellular Innovation of the Cyanobacterial Heterocyst by the Adaptive Loss of Plasticity

Cellular innovation is central to biological diversification, yet its underlying mechanisms remain poorly understood [1]. One potential source of new cellular traits is environmentally induced phenotypic variation, or phenotypic plasticity. The plasticity-first hypothesis [2-4] proposes that natural selection can improve upon an ancestrally plastic phenotype to produce a locally adaptive trait, but the role of plasticity for adaptive evolution is still unclear [5-10]. Here, we show that a structurally novel form of the heterocyst, the specialized nitrogen-fixing cell of the multicellular cyanobacterium Fischerella thermalis, has evolved multiple times from ancestrally plastic developmental variation during adaptation to high temperature. Heterocyst glycolipids (HGs) provide an extracellular gas diffusion barrier that protects oxygen-sensitive nitrogenase [11, 12], and cyanobacteria typically exhibit temperature-induced plasticity in HG composition that modulates heterocyst permeability [13, 14]. By contrast, high-temperature specialists of F. thermalis constitutively overproduce glycolipid isomers associated with high temperature to levels unattained by plastic strains. This results in a less-permeable heterocyst, which is advantageous at high temperature but deleterious at low temperature for both nitrogen fixation activity and fitness. Our study illustrates how the origin of a novel cellular phenotype by the genetic assimilation and adaptive refinement of a plastic trait can be a source of biological diversity and contribute to ecological specialization.

Heterocyte glycolipids indicate polyphyly of stigonematalean cyanobacteria

The cyanobacterial phylum is currently divided into five subsections (I-V), with the latter two containing no or false-branching (nostocalean) and true-branching (stigonematalean) cyanobacteria. Although morphological traits (such as cellular division and secondary branches) clearly separate both types of heterocytous cyanobacteria, molecular evidence indicates that stigonematalean cyanobacteria (Subsection V) do not form a monophyletic group but instead are interspersed and nested within the nostocalean cyanobacteria (Subsection IV). To further resolve the phylogeny of heterocytous cyanobacteria, we here analyzed the distribution of heterocyte glycolipids (HGs) in the true-branching cyanobacterium Stigonema ocellatum SAG 48.90 (type genus of Subsection V) and compared it with the HG inventory of other stigonematalean and nostocalean cyanobacteria. The most dominant HGs in S. ocellatum SAG 48.90 were 1-(O-hexose)-27-keto-3,25-octacosanediol (HG₂₈ keto-diol) and 1-(O-hexose)-3,25,27-octacosanetriol (HG₂₈ triol), which together constituted ca. 94% of all HGs. In addition, 1-(O-hexose)-3-keto-27-octacosanols (HG₂₈ keto-ols), 1-(O-hexose)-3,27-octacosanediols (HG₂₈ diols), 1-(O-hexose)-3-keto-27,29-triacontanediol (HG₃₀ keto-diol) and 1-(O-hexose)-3,27,29-triacontanetriol (HG₃₀ triol) occurred in minor abundances. Heterocyte glycolipids previously reported to be unique for stigonematalean cyanobacteria, i.e. 1-(O-hexose)-3,29,31-dotriacontanetriols (HG₃₂ triols) and 1-(O-hexose)-3-keto-29,31-dotriacontanediols (HG₃₂ keto-diols), were not detected in S. ocellatum SAG 48.90. Comparison of the HG distribution pattern with those of other heterocytous cyanobacteria indicated that S. ocellatum SAG 48.90 is most closely related to the nostocalean families Rivulariaceae and Scytonemataceae, which is complementary to reconstructed 16S rRNA gene sequence phylogenies. Our HG-based data thus provides evidence for the polyphyly of stigonematalean cyanobacteria, independent from molecular approaches, and points to the need for a critical re-evaluation of the current taxonomy of heterocytous cyanobacteria.