Coccoid Cyanobacteria Research Articles

Comparison of imaging flow cytometry and microscopy for freshwater algal bloom detection

Gifford SR, St. Amand A, Graham JL, Foster GM, Sauve C, Clark D, Schroeder-Larkins H. 2024. Comparison of imaging flow cytometry and microscopy for freshwater algal bloom detection. Lake Reserv Manage. 40:221–235. Imaging flow cytometry (IFC) is an emerging tool that allows for rapid identification and enumeration of phytoplankton in freshwater systems. However, few studies have assessed the effects of preservation on IFC results or compared live IFC and microscopy results in freshwater systems. Understanding the effects of preservation and differences between IFC and microscopy will improve interpretation of these data and inform strategies to use IFC-based approaches in freshwater systems. Our study objectives were to compare IFC and phase contrast with epifluorescence microscopy as techniques for phytoplankton identification and enumeration, and the effects of sample preservation with an emphasis on taxa forming harmful cyanobacterial blooms (HCBs). During June through October 2020, samples were collected from 2 lakes in the Finger Lakes region of New York. Live and preserved samples were analyzed by laboratory-based IFC, and preserved samples were analyzed by microscopy. The IFC approach captured community dynamics while detecting potential cyanobacterial bloom-forming taxa earlier and at lower abundances than microscopy. Laboratory-based IFC allowed for an intermediate level of taxonomic information when compared to microscopy, gross techniques, such as extracted chlorophyll a or fluorescence sensors, and field-based operation of IFC approaches. The laboratory-based application of IFC in this study allowed receipt of results in 5 d or less, a substantial improvement over microscopy, which can be time-consuming to conduct. However, the laboratory-based IFC approach had some limitations. Imaging flow cytometry-estimated biovolume may be less accurate than microscopy for some taxa because of the algorithms used to calculate biovolume, particularly for chrysophytes and coccoid cyanobacteria. Colonial dissociation during preservation appeared to affect detection of Microcystis by IFC less than for other fragile bloom-forming taxa like chrysophytes. Our study results advance understanding of how IFC may translate to field-based approaches for early harmful algal bloom indicators in freshwater.

Aridity modulates biogeographic distribution and community assembly of cyanobacterial morphotypes in drylands.

The patterns of biogeographic distribution and assembly processes of microbiota are of vital importance for understanding ecological adaptation and functioning maintenance. However, the role of morphological characteristics in microbial assembly is still poorly ascertained. Here, by integrating high-throughput sequencing and robust extrapolation of traits, we investigated taxonomic and phylogenetic turnovers of various cyanobacterial morphotypes in biocrusts to evaluate the contributions of deterministic and stochastic processes across a large scale of drylands in northwestern China. The results showed that the non-heterocystous filamentous category dominated biocrusts in the arid ecosystem and exhibited strong tolerance against environmental fluctuations. Despite the significant distance-decay relationship of β-diversity detected in all categories, both species composition and phylogenetic turnover rates of coccoid cyanobacteria were higher than non-heterocystous filamentous and heterocystous morphotypes. Moreover, the assembly of cyanobacteria was driven by different ecological processes that the entire community and non-heterocystous filamentous morphotype were governed by deterministic processes, while stochasticity prevailed in heterocystous and coccoid cyanobacteria. Nonetheless, aridity can modulate the balance between determinism and stochasticity and prompt a shifting threshold among morphotypes. Our findings provide a unique perspective to understanding the critical role of microbial morphology in community assembly and facilitate the prediction of biodiversity loss under climate change.

Initial Accretion in Hamelin Pool Microbialites: The Role of Entophysalis in Precipitation of Microbial Micrite

One of the largest assemblages of living marine microbialites, with shapes and sizes analogous to ancient structures, is found along the margins of Hamelin Pool, Shark Bay, Western Australia. An investigation of microbial mats on the surfaces of these structures using petrographic analysis, light, and scanning electron microscopy identified the in situ precipitation of micrite as an important accretion mechanism in all major mat types (pustular, smooth, and colloform). Within each mat type, peloidal micrite, composed of nano-bulbous spheres to tabular and rod-shaped crystals, was closely linked with cells of the coccoid cyanobacterium Entophysalis, and microtextures of the micrite reflected the size and distribution of Entophysalis colonies. In pustular surface mats, where large colonies of Entophysalis were common, large clots of micrite were distributed randomly throughout the mat. In contrast, in smooth and colloform mats, where smaller colonies of Entophysalis were distributed along horizons, micrite formed fine laminae. In all surface mat types, micrite associated with Entophysalis had a characteristic honeycomb appearance, resulting from cell and/or colony entombment. These findings redefine our understanding of microbialite accretion in Hamelin Pool, recognizing the importance of microbial micrite in microbialite growth and showing that coccoid cyanobacteria are capable of building laminated structures. Moreover, Entophysalis, the dominant visible microbe associated with the precipitation of micrite in Hamelin Pool, has a lineage to Eoentophysalis, found throughout early and middle Proterozoic microbialites assemblages. These findings reinforce the importance of Hamelin Pool as a window to the past.

New cyanobacterium Aliterella vladivostokensis sp. nov. (Aliterellaceae, Chroococcidiopsidales), isolated from temperate monsoon climate zone (Vladivostok, Russia)

A new coccoid cyanobacterium Aliterella vladivostokensis sp. nov. was described from an urban aerophytic habitat in a temperate monsoon climate (Vladivostok, Russia) using a polyphasic approach. Phylogenetic analyses based on the 16S rRNA gene sequences confirmed that our isolate was a member of the Aliterella genus clade. Aliterella species are hardly distinguishable from each other morphologically and were described from highly contrasting natural and artificial environments with only a few records from several continents. Despite high similarity of morphometric data for A. vladivostokensis and A. antarctica cells and a compensatory base change in the D1–D1′ helix shared by these species; high percent of dissimilarity (11.6±1.3) between their 16S–23S internal transcribed spacer sequences with at least 5 autapomorphic mutations in the D1–D1′ and Box-B helices, and distinct folding patterns of the Box-B helix allowed us to erect a new species.

Filamentous cyanobacteria and associated microorganisms, structurally preserved in a Late Jurassic chert from Patagonia, Argentina

A new cyanobacterium, Patagonifilum jurassicum nov. gen. et sp., is structurally preserved in Late Jurassic hydrothermally influenced siliceous chert from the Deseado Massif, Patagonia, Argentina. The cyanobacterium occurs in the form of loosely to densely spaced, heteropolar filaments (up to 4.5 μm wide) that form turf-like stands, or spherical to hemispherical colonies on different substrates, usually degraded plant stems. Filaments consist of barrel-shaped cells enveloped in a non-stratified sheath, and basal cells that are distinct. The fossil is similar to certain present-day members of the Oscillatoriales (e.g., Homoeothrix), Synechococcales (e.g., Tapinothrix), and Nostocales (e.g., Rivularia, Gloeotrichia). Associated with the cyanobacteria are spheroidal to ovoid vesicles, up to 45 μm in diameter, which occur singly or clustered, mostly near the base of the filaments. They resemble certain present-day zoosporic fungi, and algae, coccoid cyanobacteria, and possibly certain arthropod eggs; however, their systematic affinities remain unresolved. This discovery is nevertheless important because it suggests that the cyanobacterial overgrowths from the Patagonian Jurassic cherts were not monospecific, but rather comprised different organisms that perhaps even interacted with each other.

Spherulitic microbialites from modern hypersaline lakes, Rottnest Island, Western Australia.

Fibrous-radiating carbonate spherulites spatially associated with poorly crystalline Mg-Si substances have formed within conical microbialites in modern hypersaline lakes on Rottnest Island, Western Australia. Two spherulitic fabrics can be distinguished based on compositional and textural differences. The oldest (lowermost) fabric comprises variably intergrown aragonitic spherulites 100-500μm wide, containing micritic nuclei with coccoid cell molds in various stages of cell division. Spherulite matrices contain aggregates of individual nanospheres 150-200nm wide, composed of a poorly crystalline Mg-Si phase, locally containing cell molds with similar dimensions to those within spherulite nuclei. The younger (upper) fabric comprises sub-polyhedral networks of mineralized EPS composed of an Mg-Si substance. The polyhedrons contain aragonite-replaced coccoid cells, voids, and polyhedral spherulites 8-12μm wide with a morphology determined by fossil EPS, interpreted to have been produced by coccoid cyanobacteria. These spherulites are composed of high-Mg calcite, inferred to have formed in association with heterotrophic bacteria. Stable isotope data, textural relationships, and geochemical modeling are consistent with cyanobacterial oxygenic photosynthesis influencing the precipitation of Mg-Si substances and aragonitic spherulites by locally increasing the pH. The morphology of the polyhedral spherulites suggests the former presence of EPS and that faceted spherulites with similar dimensions in the geological record may represent biosignatures. The Rottnest Island conical microbialites demonstrate an intimate association between microbial features and processes and spherulitic fabrics, potentially providing insights into texturally and compositionally similar features in the geological record.

Polybessurus-like fossils as key contributors to Permian–Triassic boundary microbialites in South China

Massive occurrences of microbialites near the Permian–Triassic boundary have been interpreted as being due to benthic microbial proliferation in unusual marine conditions after the end-Permian mass extinction. Here, we present large populations of Polybessurus-like microfossils in the microbialites of the South China Craton to reveal their morphological structures, growth patterns, and ecological implications. These distinctive microfossils are composed of layered stalks and spherical endpoints. The spheroids, 20–40 μm in diameter, comprising external thin micritic walls and internal sparry parts, are interpreted as coccoid cyanobacteria. The stalks consist of multiple “stacked-cup” micritic envelopes consisting of micron-sized magnesian calcite/dolomite grains and are catalogued as calcified remains of coccoid cyanobacterial extracellular polymeric substances (EPS). Early microbially mediated calcification of EPS increased the preservation potential of microfossils. The microfossils stand upright as coccoid unicells supported by the highly unidirectional secretion of EPS, revealing their benthic behaviours. The successively secreted EPS lift the cells away from the substrate, expanding their ecological niches to gain more sunlight for photosynthesis in the barren marine floor. The distinctive Polybessurus-like microfossils can be viewed both in laminae of stromatolites and in spotted/digitate clots of thrombolites, suggesting their critical roles in microbe-dominated reefs in the aftermath of the end-Permian mass extinction. The morphological features and growth patterns of the Polybessurus-like fossils resemble their Proterozoic counterpart—Polybessurus bipartitus Fairchild ex Green et al. (1987). The widespread Polybessurus-like fossils in the Permian–Triassic boundary microbialites of the South China Craton suggest pervasive retrogressive ecosystems on carbonate platforms after the largest extinction event during the Earth's history.

The Record of Environmental and Microbial Signatures in Ancient Microbialites: The Terminal Carbonate Complex from the Neogene Basins of Southeastern Spain

The Messinian microbialites of the Terminal Carbonate Complex (TCC) from the Neogene basins of southeastern Spain show both diversified morphologies and an excellent preservation of primary microbial microstructures. Their stratigraphic architecture, fabric (micro-, meso-, and macro-fabric), and mineralogical composition were investigated in eight localities from three sedimentary basins of southeastern Spain: The Sorbas and Bajo Segura basins and the Agua Amarga depression. Two recurrent microbialite associations were distinguished. Laterally linked low relief stromatolites predominated in Microbialite Association 1 (MA1), which probably formed in low energy lagoons or lakes with fluctuating normal marine to hypersaline water. The microfabrics of MA1 reflected the predominance of microbially induced/influenced precipitation of carbonates and locally (Ca)-Mg-Al silicates. Microbialite Association 2 (MA2) developed in high energy wave and tidal influenced foreshore to shoreface, in normal marine to hypersaline water. High-relief buildups surrounded by mobile sediment (e.g., ooids or pellets) dominated in this environment. MA2 microbialites showed a significant proportion of thrombolitic mesofabric. Grain-rich microfabrics indicated that trapping and binding played a significant role in their accretion, together with microbially induced/influenced carbonate precipitation. The stratigraphic distribution of MA1 and MA2 was strongly influenced by water level changes, the morphology and nature of the substratum, and exposure to waves. MA1 favorably developed in protected areas during third to fourth order early transgression and regression phases. MA2 mostly formed during the late transgressions and early regressions in high energy coastal areas, often corresponding to fossil coral reefs. Platform scale syn-sedimentary gypsum deformation and dissolution enhanced microbial carbonate production, microbialites being thicker and more extended in zones of maximum deformation/dissolution. Microbial microstructures (e.g., microbial peloids) and microfossils were preserved in the microbialites. Dolomite microspheres and filaments showed many morphological similarities with some of the cyanobacteria observed in modern open marine and hypersaline microbialites. Dolomite potentially replaced a metastable carbonate phase during early diagenesis, possibly in close relationship with extracellular polymeric substances (EPS) degradation. Double-layered microspheres locally showed an inner coating made of (Ca)-Mg-Al silicates and carbonates. This mineral coating could have formed around coccoid cyanobacteria and indicated an elevated pH in the upper part of the microbial mats and a potential dissolution of diatoms as a source of silica. Massive primary dolomite production in TCC microbialites may have resulted from enhanced sulfate reduction possibly linked to the dissolving gypsum that would have provided large amounts of sulfate-rich brines to microbial mats. Our results open new perspectives for the interpretation of ancient microbialites associated with major evaporite deposits, from microbe to carbonate platform scales.

The Relative Importance of Shear Forces and Surface Hydrophobicity on Biofilm Formation by Coccoid Cyanobacteria.

Understanding the conditions affecting cyanobacterial biofilm development is crucial to develop new antibiofouling strategies and decrease the economic and environmental impact of biofilms in marine settings. In this study, we investigated the relative importance of shear forces and surface hydrophobicity on biofilm development by two coccoid cyanobacteria with different biofilm formation capacities. The strong biofilm-forming Synechocystis salina was used along with the weaker biofilm-forming Cyanobium sp. Biofilms were developed in defined hydrodynamic conditions using glass (a model hydrophilic surface) and a polymeric epoxy coating (a hydrophobic surface) as substrates. Biofilms developed in both surfaces at lower shear conditions contained a higher number of cells and presented higher values for wet weight, thickness, and chlorophyll a content. The impact of hydrodynamics on biofilm development was generally stronger than the impact of surface hydrophobicity, but a combined effect of these two parameters strongly affected biofilm formation for the weaker biofilm-producing organism. The antibiofilm performance of the polymeric coating was confirmed at the hydrodynamic conditions prevailing in ports. Shear forces were shown to have a profound impact on biofilm development in marine settings regardless of the fouling capacity of the existing flora and the hydrophobicity of the surface.

Morphological identification, isolation, and culturing of cyanobacteria derived from hot spring of Cisolok and Galunggung Mountain based on enrichment method

Research on isolating and culturing of cyanobacteria from hot springs of Cisolok and Galunggung Mountain in West Java Indonesia had been done. This research was a study to find a fast and accurate method to identify, isolate and culture the cyanobacteria originating from extreme region, especially from the hot springs. Identification based on morphological characters performed in line with the process of isolation of the founded cyanobacteria strains. In the process of isolation, enrichment methods carried out in stages to determine the viability of each strain to be easily cultured (culturable). Four (4) types of media used in this study, i.e. BBM, BG-11, CT and MA. Pipette method was used to create a single culture. At the initial observations of the fresh samples, 3 types of cyanobacteria thallus were found, i.e. the form of thread/filament (unbranched filament), branched filament, and rounded shapes (coccoid). Furthermore, from all the enrichment samples (stage-1 and stage-2), 12 genera of cyanobacteria were found, i.e. Leptolyngbya, Gloeocapsa, Chroococcus, Oscillatoria, Synechococcus, Fischerella, Scytonema, Hapalosiphon, Microcystis, Nostoc, Gloeotrichia, and Stanieria. In the first stage of enrichment culture samples of Cisolok, eight (8) genera were found, i.e. Leptolyngbya, Chroococcus, Oscillatoria, Synechococcus, Scytonema, Hapalosiphon, Nostoc, and Gloeotrichia, while in the hot spring of Galunggung mountain, only four (4) genera were found (Leptolyngbya, Oscillatoria, Hapalosiphon, and Nostoc). There were several filaments and coccoid cyanobacteria that could not be identified by morphological characters. Meanwhile, in the second stage of enrichment culture samples of Cisolok, nine (9) genera were found, i.e. six (6) genera similar to those found in the first stage of enrichment (Leptolyngbya, Chroococcus, Oscillatoria, Synechococcus, Scytonema, Hapalosiphon), and added with the genus of Gloeocapsa, Microcystis, and Stanieria. From the hot spring of Mt Galunggung, nine (9) genera were found, i.e. four (4) genera similar to those found in the first stage of enrichment (Leptolyngbya, Oscillatoria, Hapalosiphon, and Nostoc), and added with the genus of Chroococcus, Gloeocapsa, Microcystis, Synechococcus, and Fischerella. Both from Cisolok and from Galunggung, the three genera (Leptolyngbya, Oscillatoria, Hapalosiphon) could be found in fresh samples and enrichment samples (stage-1 and stage-2). The research concluded that the enrichment process in stages (first and second) can be used for the isolation of strains of cyanobacteria to be adaptable, and therefore easy to be cultured (culturable). The genus Scytonema and Gloeotrichia are genera that known to be difficult to be cultured, and in this study, they grow only in stage-1, while the genus Stanieria appears in stage-2. Isolates obtained consist of 31 strains from Cisolok hot spring, and 13 strains from Galunggung mountain hot spring, then would be identified (re-identification) using molecular characters (16S rDNA).

Thrombolitic clots dominated by filamentous cyanobacteria and crusts of radio-fibrous calcite in the Furongian Changshan Formation, North China

As a variety of non-laminated microbial carbonate or calcified microbialite, thrombolites commonly comprise diffusely clotted micrites as their basic structural unit. The current study is aimed at discussing the composition and forming mechanism of thrombolitic clots, which most likely represent the product formed by calcification of extracellular polymeric substances. It provides instances of sophisticated calcification of thrombolite-forming microbial mat in the calcite sea that is expressed by the distinctive composition of thrombolites. Thrombolites in the top part of the Furongian Changshan Formation are chiefly composed of chaotic large and small micritic clots as observed under low microscopic resolution. However, high density preservation of fossils of calcified sheaths of cyanobacteria is observed within most of the clots under higher resolution. Their distribution as groups or colonies suggests that they can be interpreted as Subtifloria of Girvanella group. These microbial components together with the enigmatic Epiphyton reflect fundamental features of microbial growth, and suggest a microbial origin of these clots. The general abundance of these calcified fossils within individual clots offers an instance for the formation of thrombolitic clots from sophisticated calcification of photosynthetic biofilms. It refutes the traditional view that both the thrombolites and the oncoids develop by accretion of microbial mats dominated by coccoid cyanobacteria. Aggregation of several individual clots to form millimetric agglutinated clots shows that their formation is genetically related to sophisticated calcification of extracellular polymeric substances making up multiple biofilms within relatively thick microbial mats. This inference is strengthened by their encrustation by radio-fibrous calcite, which leads to enlargement of the clots. Besides the clots, benthic ooids, pyrite and dolomite also developed in the current thrombolites, which are largely attributed to microbially mediated organomineralization.

Raman spectroscopic screening of cyanobacterial chasmoliths from crystalline gypsum—The Messinian crisis sediments from Southern Sicily

AbstractThis study shows the first results on Raman spectroscopic investigations of pigments from cyanobacterial endolithic colonisations in gypsum of Messinian age (Miocene). Gypsum from outcrops of sedimentary series close to Eraclea Minoa (Sothern Sicily) is sometimes inhabited by endoliths. Raman spectroscopic investigations allow to specify type of colonisation through identification of their pigments. Coccoid cyanobacteria (Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Synechococcus sciophilus), filamentous heterocytous Nostoc sp., and filamentous bundle‐forming Symplocastrum cf. aurantiacum and Microcoleus sp. were found to inhabit different parts of the gypsum samples. Carotenoids (as assumed frequently β‐carotene) are produced in all the samples studied (optimised detection using 514‐nm excitation), scytonemin in the samples colonised by G. pleurocapsoides (G1, G2, and G6), and phycobiliproteins in the sample G3 (those detected using 785‐nm excitation). This study is the first initiative to collect better knowledge on detecting biomarker traces in the frame of Messinian‐age gypsum sequence of relevance for old Martian environments.

A coccoid, colony-forming cyanobacterium from the Lower Devonian Rhynie chert that resembles Eucapsis (Synechococcales) and Entophysalis (Chroococcales)

The Rhynie chert provides sublime fossils of cyanobacteria from an Early Devonian hot spring ecosystem. However, only a small fraction of the diversity has been documented. Rhyniotaxillus devonicus nov. gen. et sp., a minute coccoid cyanobacterium from the Rhynie chert, is characterized by cuboid to somewhat irregular colonies of up to 64 cells (cell diameter: 2.5–3.5 μm) arranged into sarcinoid packages, and held together by prominent gelatinous envelopes. Colony morphology parallels that seen in certain present-day species of Eucapsis (Synechococcales) and Entophysalis (Chroococcales), as well as Eoentophysalis belcherensis, a Precambrian fossil equivalent of Entophysalis. The systematic affinities of R. devonicus remain unresolved. Nevertheless, this discovery expands our knowledge of cyanobacterial diversity in early non-marine ecosystems.

Cyanidium chilense (Cyanidiophyceae, Rhodophyta) from tuff rocks of the archeological site of Cuma, Italy

SUMMARYPhlegrean Fields is a large volcanic area situated southwest of Naples (Italy), including both cave and thermoacidic habitats. These extreme environments host the genus Cyanidium; the species C. chilense represents a common phototrophic microorganism living in anthropogenic caves. With a view to provide a comprehensive characterization for a correct taxonomic classification, morpho‐ultrastructural investigations of C. chilense from Sybil's cave (Phlegren Fields) was herein carried out and compared with the thermoacidophilic C. caldarium. The biofilm was also analyzed to define the role of C. chilense in the establishment of a biofilm within cave environments. Despite the peculiar ecological and molecular divergences, C. chilense and C. caldarium shared all the main diacritic features, suggesting morphological convergence within the genus; cytological identity was found among C. chilense strains geographically distant and adapted to different substrates, such as the porous yellow tuff of Sybil cave, and calcyte, magnesite and basaltic rocks from other caves. C. chilense is generally dominant in all biofilms, developing monospecific islets, developing both superficially or between fungal hyphae and coccoid cyanobacteria. Extracellular polymeric substances (EPS) were recorded in C. chilense biofilms from Sybil cave, confirming the role of EPS in facilitating cells adhesion to the surface, creating a cohesive network of interconnecting biofilm cells.

In this Issue

i DOI: https://doi.org/10.3318/BIOE.2019.05 Biology and Environment: Proceedings of the Royal Irish Academy,Vol. 119, No. 1, i–ii (2019). © Royal Irish Academy Cite as follows: Osborne, B. 2019 Editorial / In this Issue. Biology and Environment: Proceedings of the Royal Irish Academy 2019. DOI: 10.33318/ BIOE.2019.05 EDITORIAL Bruce Osborne Despite the challenging times we live in with an­ ever-increasing number of journals plying for ­ papers in the biological and environmental areas,I am pleased to say that Biology and Environment is maintaining our impact factor above 0.65 (0.676). Whilst this is the good news,maintaining or even increasing our impact factor in the future is a significant challenge so we need to continue to ensure that we receive high-quality submissions.As editor a particular onus is placed on me, together with the other members of the editorial board, to ensure that this happens. We are, however, always open to new ideas and new publication initiatives that will increase the journal’s impact and readership and I would encourage, in particular, suggestions for new Praeger Reviews and special issues. In terms of new initiatives this issue contains the first of what I hope will be a series of so-called ‘data papers’.This initiative is based on the increasing body of numerical information that is often not suitable for more conventional publications as it is not specifically hypothesis-driven research. Nevertheless , well-documented metadata is an important and often essential resource for informing current and future research as well as providing the basis for wider collaborative initiatives. Moreover, these publications provide a way of recognising all those who contributed to the collection, management and curation of the data sets. I hope, therefore, that this is a publication opportunity that a number of you can take advantage of in the future. I would like finally to recognise all the Royal Irish Academy staff, editorial board members and reviewers who have contributed to Biology and Environment over the past year. Bruce Osborne IN THIS ISSUE Limestone lake crusts Limestone lakes are often characterised by a benthos consisting of charophyte algae and a microbial crust comprising of a range of microbes intermixed with inorganic minerals.Whilst the more visible charophyte beds have received considerable attention much less is known about the functional significance and formation of the microbial crusts. Doddy et al., in this issue point out that although these crusts are sometimes considered as largely inert inorganic minerals,they are complex substrates containing a diverse assemblage of living microorganisms. Both filamentous and coccoid cyanobacteria are present as are chlorophytes and diatoms that reflect, in part, the organisms present in the water column.As expected the crusts contain a high proportion of mineral particles that may be cemented together through the actions of filamentous cyanobacteria.In terms of the controls over crust formation Doddy et al. provide evidence that this is related to P availability, with crust deterioration evident at high water column P concentrations . Crusts may also act as a significant sink for P so that conservation of these habitats should consider any effects that impact on their functionality, including increased turbidity and modifications in water chemistry. Importantly, as improvements in water column quality may not be synonymous with improvements in the status of the microbial crusts, specific conservation measures are likely to be required that are targeted directly at the benthic community. Cattle impacts on the hyporheic zone The word hyporheic, from the Greek hypo (below) and rheos (flow), was first coined by the Romanian hydrobiologist Traian Orghidan in 1955 to denote the area below the stream bed where mixing of surface and ground water occurs.This is an important interface often characterised by a unique assemblage of organisms that control the exchange of organic material, water and nutrients between surface and ground water bodies. Importantly this zone can be strongly impacted by agricultural activity, as­ O’Sullivan et al., in this issue, show.The authors detail how cattle access to the shallow areas associated with headwater streams can increase downstream sediment flow and negatively impact on hyporheic invertebrate communities. In some cases this also resulted in a reduction...

In this Issue

i DOI: https://doi.org/10.3318/BIOE.2019.05 Biology and Environment: Proceedings of the Royal Irish Academy,Vol. 119, No. 1, i–ii (2019). © Royal Irish Academy Cite as follows: Osborne, B. 2019 Editorial / In this Issue. Biology and Environment: Proceedings of the Royal Irish Academy 2019. DOI: 10.33318/ BIOE.2019.05 EDITORIAL Bruce Osborne Despite the challenging times we live in with an­ ever-increasing number of journals plying for ­ papers in the biological and environmental areas,I am pleased to say that Biology and Environment is maintaining our impact factor above 0.65 (0.676). Whilst this is the good news,maintaining or even increasing our impact factor in the future is a significant challenge so we need to continue to ensure that we receive high-quality submissions.As editor a particular onus is placed on me, together with the other members of the editorial board, to ensure that this happens. We are, however, always open to new ideas and new publication initiatives that will increase the journal’s impact and readership and I would encourage, in particular, suggestions for new Praeger Reviews and special issues. In terms of new initiatives this issue contains the first of what I hope will be a series of so-called ‘data papers’.This initiative is based on the increasing body of numerical information that is often not suitable for more conventional publications as it is not specifically hypothesis-driven research. Nevertheless , well-documented metadata is an important and often essential resource for informing current and future research as well as providing the basis for wider collaborative initiatives. Moreover, these publications provide a way of recognising all those who contributed to the collection, management and curation of the data sets. I hope, therefore, that this is a publication opportunity that a number of you can take advantage of in the future. I would like finally to recognise all the Royal Irish Academy staff, editorial board members and reviewers who have contributed to Biology and Environment over the past year. Bruce Osborne IN THIS ISSUE Limestone lake crusts Limestone lakes are often characterised by a benthos consisting of charophyte algae and a microbial crust comprising of a range of microbes intermixed with inorganic minerals.Whilst the more visible charophyte beds have received considerable attention much less is known about the functional significance and formation of the microbial crusts. Doddy et al., in this issue point out that although these crusts are sometimes considered as largely inert inorganic minerals,they are complex substrates containing a diverse assemblage of living microorganisms. Both filamentous and coccoid cyanobacteria are present as are chlorophytes and diatoms that reflect, in part, the organisms present in the water column.As expected the crusts contain a high proportion of mineral particles that may be cemented together through the actions of filamentous cyanobacteria.In terms of the controls over crust formation Doddy et al. provide evidence that this is related to P availability, with crust deterioration evident at high water column P concentrations . Crusts may also act as a significant sink for P so that conservation of these habitats should consider any effects that impact on their functionality, including increased turbidity and modifications in water chemistry. Importantly, as improvements in water column quality may not be synonymous with improvements in the status of the microbial crusts, specific conservation measures are likely to be required that are targeted directly at the benthic community. Cattle impacts on the hyporheic zone The word hyporheic, from the Greek hypo (below) and rheos (flow), was first coined by the Romanian hydrobiologist Traian Orghidan in 1955 to denote the area below the stream bed where mixing of surface and ground water occurs.This is an important interface often characterised by a unique assemblage of organisms that control the exchange of organic material, water and nutrients between surface and ground water bodies. Importantly this zone can be strongly impacted by agricultural activity, as­ O’Sullivan et al., in this issue, show.The authors detail how cattle access to the shallow areas associated with headwater streams can increase downstream sediment flow and negatively impact on hyporheic invertebrate communities. In some cases this also resulted in a reduction...

Microbialite crusts in Irish limestone lakes reflect lake nutrient status

Many Irish limestone lakes contain a characteristic benthic crust, a microbialite layer composed of cyanobacteria, algae and inorganic mineral deposits. Previous work suggests that these crusts are influenced by lake nutrient status. The purpose of this paper was to test this hypothesis. In order to do this, it was first necessary to describe crust structure, chlorophyll content and species composition. Relative abundances of species were examined, as well as crust cover, thickness and organic content. A diverse community of filamentous and coccoid cyanobacteria was recorded, with chlorophytes and diatoms also present. Crusts were found to contain a high percentage (>75% of dry mass) of mineral particles, bound together by various filamentous cyanobacteria. Significant differences were shown between lakes of different trophic states, based on analyses of biological and physical factors. Strong correlations were found between total P, crust chlorophyll and crust community structure.

Microbialite crusts in Irish limestone lakes reflect lake nutrient status

Many Irish limestone lakes contain a characteristic benthic crust, a microbialite layer composed of cyanobacteria, algae and inorganic mineral deposits. Previous work suggests that these crusts are influenced by lake nutrient status. The purpose of this paper was to test this hypothesis. In order to do this, it was first necessary to describe crust structure, chlorophyll content and species composition. Relative abundances of species were examined, as well as crust cover, thickness and organic content. A diverse community of filamentous and coccoid cyanobacteria was recorded, with chlorophytes and diatoms also present. Crusts were found to contain a high percentage (>75% of dry mass) of mineral particles, bound together by various filamentous cyanobacteria. Significant differences were shown between lakes of different trophic states, based on analyses of biological and physical factors. Strong correlations were found between total P, crust chlorophyll and crust community structure.

Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus

Many cyanobacteria, which use light as an energy source via photosynthesis, have evolved the ability to guide their movement toward or away from a light source. This process, termed "phototaxis," enables organisms to localize in optimal light environments for improved growth and fitness. Mechanisms of phototaxis have been studied in the coccoid cyanobacterium Synechocystis sp. strain PCC 6803, but the rod-shaped Synechococcus elongatus PCC 7942, studied for circadian rhythms and metabolic engineering, has no phototactic motility. In this study we report a recent environmental isolate of S. elongatus, the strain UTEX 3055, whose genome is 98.5% identical to that of PCC 7942 but which is motile and phototactic. A six-gene operon encoding chemotaxis-like proteins was confirmed to be involved in phototaxis. Environmental light signals are perceived by a cyanobacteriochrome, PixJSe (Synpcc7942_0858), which carries five GAF domains that are responsive to blue/green light and resemble those of PixJ from Synechocystis Plate-based phototaxis assays indicate that UTEX 3055 uses PixJSe to sense blue and green light. Mutation of conserved functional cysteine residues in different GAF domains indicates that PixJSe controls both positive and negative phototaxis, in contrast to the multiple proteins that are employed for implementing bidirectional phototaxis in Synechocystis.

Primary productivity of coccoid cyanobacteria isolated from a coastal lagoon environment south of the Gulf of California.

The objective of this study was to determine the primary productivity of cyanobacteria grown under different nitrogen sources. 3 treatments were considered: 1) without a nitrogen source, 2) with nitrate (NO3), and 3) with ammonium (NH4). Incubations were carried out under controlled conditions. Cell densities were significantly higher in nitrate treatment. The maximums of biovolume (19.9 µm-3) and of carbon content (5.4 pg C cel-1) were observed in the stationary phase of the treatment with ammonia. The highest concentration of chlorophyll a in the exponential phase was recorded in the treatment without nitrogen (1,038 mg m-3), while the maximum in the stationary phase in the treatment with nitrates (0.65 mg m-3). The highest primary production was recorded in the exponential phase (23.9 mg C m-3 h-1), associated with treatment without a nitrogen source incubated at 150 µ E m-2 s-1; in the stationary phase the maximum (11.6 mg C m-3 h-1) was registered in the treatment enriched with nitrates at 75 µ E m-2 s-1.