Microbial Blooms Research Articles

Effect of a giant meteorite impact on Paleoarchean surface environments and life

Large meteorite impacts must have strongly affected the habitability of the early Earth. Rocks of the Archean Eon record at least 16 major impact events, involving bolides larger than 10 km in diameter. These impacts probably had severe, albeit temporary, consequences for surface environments. However, their effect on early life is not well understood. Here, we analyze the sedimentology, petrography, and carbon isotope geochemistry of sedimentary rocks across the S2 impact event (37 to 58 km carbonaceous chondrite) forming part of the 3.26 Ga Fig Tree Group, South Africa, to evaluate its environmental effects and biological consequences. The impact initiated 1) a giant tsunami that mixed Fe2+-rich deep waters into the Fe2+-poor shallow waters and washed debris into coastal areas, 2) heating that caused partial evaporation of surface ocean waters and likely a short-term increase in weathering and erosion on land, and 3) injection of P from vaporization of the S2 bolide. Strata immediately above the S2 impact event contain abundant siderites, which are associated with organic matter and exhibit light and variable δ13Ccarb values. This is consistent with microbial iron cycling in the wake of the impact event. Thus, the S2 impact likely had regional, if not global, positive and negative effects on life. The tsunami, atmospheric heating, and darkness would likely have decimated phototrophic microbes in the shallow water column. However, the biosphere likely recovered rapidly, and, in the medium term, the increase in nutrients and iron likely facilitated microbial blooms, especially of iron-cycling microbes.

Control of cyanobacterial growth with potassium; implications for bloom control in nuclear storage ponds

Microbial blooms have been reported in the First Generation Magnox Storage Pond at the Sellafield Nuclear Facility. The pond is kept alkaline with NaOH to minimise fuel rod corrosion, however alkali-tolerant microbial blooms dominated by the cyanobacterium Pseudanabaena catenata are able to thrive in this hostile environment. This study assessed the impact of alternative alkali-dosing regimens (KOH versus NaOH treatment) on biomass accumulation, using a P. catenata dominated mixed culture, which is representative of the pond environment. Optical density was reduced by 40–67 % with KOH treatment over the 3-month chemostat experiment. Microbial community analysis and proteomics demonstrated that the KOH-dependent inhibition of cell growth was mostly specific to P. catenata. The addition of KOH to nuclear storage ponds may therefore help control growth of this pioneer photosynthetic organism due to its sensitivity to potassium, while maintaining the high pH needed to inhibit the corrosion of stored nuclear fuel.

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet.

Microbial blooms colonize the Greenland Ice Sheet bare ice surface during the ablation season and significantly reduce its albedo. On the ice surface, microbes are exposed to high levels of irradiance, freeze-thaw cycles, and low nutrient concentrations. It is well known that microorganisms secrete metabolites to maintain homeostasis, communicate with other microorganisms, and defend themselves. Yet, the exometabolome of supraglacial microbial blooms, dominated by the pigmented glacier ice algae Ancylonema alaskanum and Ancylonema nordenskiöldii, remains thus far unstudied. Here, we use a high-resolution mass spectrometry-based untargeted metabolomics workflow to identify metabolites in the exometabolome of microbial blooms on the surface of the southern tip of the Greenland Ice Sheet. Samples were collected every 6 h across two diurnal cycles at 5 replicate sampling sites with high similarity in community composition, in terms of orders and phyla present. Time of sampling explained 46% (permutational multivariate analysis of variance [PERMANOVA], pseudo-F = 3.7771, p = 0.001) and 27% (PERMANOVA, pseudo-F = 1.8705, p = 0.001) of variance in the exometabolome across the two diurnal cycles. Annotated metabolites included riboflavin, lumichrome, tryptophan, and azelaic acid, all of which have demonstrated roles in microbe-microbe interactions in other ecosystems and should be tested for potential roles in the development of microbial blooms on bare ice surfaces.

Revisiting the Yudongzi microbialites (basal Triassic, northwestern Sichuan, South China): Fabric textures and paleoenvironmental implication

Unusual sedimentary deposits such as stromatolites, thrombolites, dendrolites, and giant ooids are widely distributed in the Permian–Triassic boundary (PTB) successions of shallow platform facies worldwide. These microbial fabrics, however, are rarely present in the same section. The genesis of these PTB microbialites and the oceanographic conditions linking to the end-Permian mass extinction still remain disputed despite intense study. Here, we report a stromatolite-dendrolite-thrombolite-giant ooid association from the PTB beds of the Yudongzi section on the northwestern margin of the Yangtze Platform, South China, which was situated in low latitudes during the Permian-Triassic (P-Tr) transition. The Yudongzi microbialites rest on an irregular contact with underlying Permian bioclastic limestone and are comprised of lower bedded stromatolite, digitate dendrolite, upper bedded stromatolite, and thrombolite units. The bedded stromatolite is characterized by undulating laminated structures and various amalgamated and layered clots. The digitate dendrolite is made up of digitate-like branches, formed by clots distributed in an arched arrangement, and characterized by abundant branching dendroids. The thrombolite displays distinct clotted textures that comprise a mixture of dark-colored microbial fabric and light-colored interstitial sediment. In microbialite, columnar structures identified as Gakhumella-like calcimicrobe are very abundant. Each individual of Gakhumella-like structure has densely arranged segments forming a columnar- to fan-shaped micro-structure. Single segments are arch-shaped and form a thin chamber between segments. Coccoid-like, bacterial clump-like, and other spheroidal aggregates are also commonly present and suggestive of a biogenetic origin for the Yudongzi microbialites. Moreover, distinct aragonite crystal fans are also for the first time found in the PTB microbialites in South China, suggesting that the fans may have resulted from high inorganic carbon concentrations, and thus high levels of carbonate dioxide in the seawater. The Yudongzi microbialites are capped by shelly grainstone and a massive giant oolite, implying that the demise of the Yudongzi microbialites may be due to destruction by strong wave currents in a high energy setting. Some ooids are coated unevenly by micritic laminae (or envelopes) indicating the possibility of a microbe-related origin. These microbial-coated giant ooids, together with the massive microbialites, may imply the long-term of microbial bloom in the oceans immediately after the end-Permian extinction. The co-existence of abundant Gakhumella-like microorganisms and oxygen-dependent invertebrates, together with some coccoid-like spheroids, aragonite cement crystal fans, and pyrite framboids indicative of oxygen-poor conditions, implies that oxygenation state of the PTB microbialites is much more complex than previously recognized, demonstrating need for continued multidisciplinary examination of facies changes associated biotic mass extinction.

Temporal dynamics of microbe-virus interactions in the Baltic Sea

Bacteria and archaea are key drivers of all major element cycles. Viruses that infect bacteria and archaea also play a fundamental role by altering the metabolic state of their host during infection and causing cell death. The CRISPR-Cas system is one of many strategies employed by bacteria and archaea to defend against viral infection. Invading viral DNA is incorporated into a CRISPR array as a short sequence (spacer) that is then recognised during the next viral encounter providing an adaptive immunity. The temporal dynamics of this system in the environment, however, is not well constrained. Using a meta-omic dataset spanning several years of sampling, we leveraged the CRISPR-Cas system to explore microbe-virus interactions in the Baltic Sea. Our goal was to understand how quickly microbes in the environment adapt to virus predation, and conversely how quickly viruses adapt to the microbial defence mechanism by developing mutations in the spacer-targeted region. To explore these interactions, we first generated a database consisting of thousands of complete and high-quality viral genomes recovered from viromes collected from the Baltic Sea. CRISPR arrays were then identified in microbial metagenome assembled genomes (MAGs), metagenomic contigs, and unassembled metagenomic reads from corresponding sampling time points. Virus-host dynamics were uncovered by matching quality-filtered spacers from CRISPR arrays to the viral database. The results show that spacer turnover over time can be captured in temporal meta-omic datasets. In the Baltic Sea, this has implications for the termination of microbial blooms, biogeochemical cycling, and resource turnover.

Identification of algal rich microbial blooms in the Sellafield Pile Fuel Storage Pond and the application of ultrasonic treatment to control the formation of blooms.

The presence of microorganisms in a range of nuclear facilities has been known for many years. In this study the microbial community inhabiting the Pile Fuel Storage Pond (PFSP), which is a legacy open-aired facility on the Sellafield nuclear site, Cumbria, UK, was determined to help target microbial bloom management strategies in this facility. The PFSP is currently undergoing decommissioning and the development of prolonged dense microbial blooms reduces the visibility within the water. Such impairment in the pond water visibility can lead to delays in pond operations, which also has financial implications. Efforts to control the microbial population within the PFSP are ongoing, with the installation of ultrasonic treatment units. Here next generation sequencing techniques focussing on broad targets for both eukaryotic and prokaryotic organisms were used to identify the microbial community. On-site monitoring of photosynthetic pigments indicated when microbial blooms formed and that eukaryotic algae were most likely to be responsible for these events. The sequencing data suggested that the blooms were dominated by members of the class Chrysophyceae, a group of golden algae, while evidence of cyanobacteria and other photosynthetic bacteria was limited, further supporting eukaryotic organisms causing the blooms. The results of sequencing data from 2018 was used to inform a change in the operational settings of the ultrasonic units, while monitoring of the microbial community and photosynthetic pigments trends was extended. Since the changes were made to the ultrasonic treatment, the visibility in the pond was significantly improved, with an absence of a spring bloom in 2020 and an overall reduction in the number of days lost due to microbial blooms annually. This work extends our knowledge of the diversity of microbes able to colonise nuclear fuel storage ponds, and also suggests that sequencing data can help to optimise the performance of ultrasonic treatments, to control algal proliferation in the PFSP facility and other inhospitable engineered systems.

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.

Evaluation of the impact of formaldehyde fumigation during the hatching phase on contamination in the hatch cabinet and early performance in broiler chickens

Commercial hatch cabinet environments promote replication of microorganisms. These pathogenic or apathogenic microorganisms may serve as pioneer colonizers of the gastrointestinal tract (GIT) of poultry. Some of these pioneer colonizers, such as Escherichia coli and Enterococcus spp., are opportunistic pathogens that lead to reduced performance in commercial poultry. Effective hatchery sanitation is imperative to limit contamination of naïve neonatal chicks and poults. Formaldehyde fumigation has been traditionally used to reduce the pathogen load in commercial hatch cabinets. To investigate potential alternatives to formaldehyde fumigation, models to mimic the microbial bloom in a laboratory setting must be utilized. The purpose of the present study was to evaluate the impact of a multispecies environmental challenge model (PM challenge) with and without formaldehyde fumigation during the hatching phase on early performance in broiler chicks. Three experiments were conducted to evaluate microbial contamination in the hatch cabinet environment (air samples, fluff samples), enteric colonization at day-of-hatch (DOH), and 7-day performance. In all experiments, significantly (P < 0.05) more gram-negative bacteria were recovered from the GIT at DOH in the PM challenge control group as compared to the nonchallenged control (NC) group and the formaldehyde-treated group (PM+F). There were no statistical differences in 7-day body weight gain or feed conversion ratio between the PM challenge control group, the NC group or the PM+F group. These data suggest this model could be utilized to evaluate alternatives to formaldehyde fumigation for controlling the microbial load during the hatching phase in a laboratory setting.

The interplay between Cs and K in Pseudanabaena catenata; from microbial bloom control strategies to bioremediation options for radioactive waters

Pseudanabaena dominates cyanobacterial blooms in the First-Generation Magnox Storage Pond (FGMSP) at a UK nuclear site. The fission product Cs is a radiologically significant radionuclide in the pond, and understanding the interactions between Cs and Pseudanabaena spp. is therefore important for determining facility management strategies, as well as improving understanding of microbiological responses to this non-essential chemical analogue of K. This study evaluated the fate of Cs following interactions with Pseudanabaena catenata, a laboratory strain most closely related to that dominating FGMSP blooms. Experiments showed that Cs (1 mM) exposure did not affect the growth of P. catenata, while a high concentration of K (5 mM) caused a significant reduction in cell yield. Scanning transmission X-ray microscopy elemental mapping identified Cs accumulation to discrete cytoplasmic locations within P. catenata cells, indicating a potential bioremediation option for Cs. Proteins related to stress responses and nutrient limitation (K, P) were stimulated by Cs treatment. Furthermore, selected K+ transport proteins were mis-regulated by Cs dosing, which indicates the importance of the K+ transport system for Cs accumulation. These findings enhance understanding of Cs fate and biological responses within Pseudanabaena blooms, and indicate that K exposure might provide a microbial bloom control strategy.

Real-time bioelectronic sensing of environmental contaminants.

Real-time chemical sensing is crucial for applications in environmental and health monitoring1. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal2-4. However, the process of protein expression limits the speed of this sensing to approximately half an hour, and optical signals are often difficult to detect in situ5-8. Here we combine synthetic biology and materials engineering to develop biosensors that produce electrical readouts and have detection times of minutes. We programmed Escherichia coli to produce an electrical current in response to specific chemicals using a modular, eight-component, synthetic electron transport chain. As designed, this strain produced current following exposure to thiosulfate, an anion that causes microbial blooms, within 2 min. This amperometric sensor was then modified to detect an endocrine disruptor. The incorporation of a protein switch into the synthetic pathway and encapsulation of the bacteria with conductive nanomaterials enabled the detection of the endocrine disruptor in urban waterway samples within 3 min. Our results provide design rules to sense various chemicals with mass-transport-limited detection times and a new platform for miniature, low-power bioelectronic sensors that safeguard ecological and human health.

Intensified microbial sulfate reduction in the deep Dead Sea during the early Holocene Mediterranean sapropel 1 deposition.

The hypersaline Dead Sea and its sediments are natural laboratories for studying extremophile microorganism habitat response to environmental change. In modern times, increased freshwater runoff to the lake surface waters resulted in stratification and dilution of the upper water column followed by microbial blooms. However, whether these events facilitated a microbial response in the deep lake and sediments is obscure. Here we investigate archived evidence of microbial processes and changing regional hydroclimate conditions by reconstructing deep Dead Sea chemical compositions from pore fluid major ion concentration and stable S, O, and C isotopes, together with lipid biomarkers preserved in the hypersaline deep Dead Sea ICDP‐drilled core sediments dating to the early Holocene (ca. 10,000 years BP). Following a significant negative lake water balance resulting in salt layer deposits at the start of the Holocene, there was a general period of positive net water balance at 9500–8300 years BP. The pore fluid isotopic composition of sulfate exhibit evidence of intensified microbial sulfate reduction, where both δ34S and δ18O of sulfate show a sharp increase from estimated base values of 15.0‰ and 13.9‰ to 40.2‰ and 20.4‰, respectively, and a δ34S vs. δ18O slope of 0.26. The presence of the n‐C17 alkane biomarker in the sediments suggests an increase of cyanobacteria or phytoplankton contribution to the bulk organic matter that reached the deepest parts of the Dead Sea. Although hydrologically disconnected, both the Mediterranean Sea and the Dead Sea microbial ecosystems responded to increased freshwater runoff during the early Holocene, with the former depositing the organic‐rich sapropel 1 layer due to anoxic water column conditions. In the Dead Sea prolonged positive net water balance facilitated primary production and algal blooms in the upper waters and intensified microbial sulfate reduction in the hypolimnion and/or at the sediment–brine interface.

Microbial Blooms Triggered Pyrite Framboid Enrichment and Oxygen Depletion in Carbonate Platforms Immediately After the Latest Permian Extinction

AbstractRedox variations across the Permian‐Triassic boundary (PTB) have long been debated, especially during the proliferation of PTB microbialites. Here, we report redox fluctuations across the PTB to evaluate links between the two based on pyrite framboid analysis from basin to platform settings in South China. During the end‐Permian extinction, abundant framboids indicate a widespread anoxia that was likely a direct cause of extinction. In the earliest Triassic (Hindeodus parvus conodont zone), pyrite framboids were absent in ramp to basin and shallow, nonmicrobialite platform sections. In contrast, the coeval microbialites yield abundant framboids indicative of dysoxia. The fact that framboids were only confined to PTB microbialites and absent in other habitats indicates that microbe bloom may have stimulated dysoxic watermass and triggered the framboid growth within microbe aggregates. Thus, microbialites were not built in reducing settings, but instead, microbial proliferation caused local, dysoxia within shallow oxygenated platforms after the extinction.

Development of an environmental contamination model to simulate the microbial bloom that occurs in commercial hatch cabinets

Microbial blooms that emerge in commercial hatch cabinets consist of apathogenic and pathogenic microorganisms, including Escherichia coli, Enterococcus faecalis, and Aspergillus fumigatus. Objectives of the present study included the development of a multipathogen contamination model to mimic commercial conditions and optimization of sampling methods to quantify bacterial or fungal presence within the hatch cabinet. The pathogen challenge mix (PM) was recreated from select bacterial or fungal isolates recovered from an egg homogenate (EH) derived from the contents of infertile eggs and late embryonic mortalities. Isolates selected for PM included Enterococcus faecalis (∼108 CFU/egg), Staphylococcus aureus (∼107 CFU/egg), Staphylococcus chromogenes (∼107 CFU/egg), Aspergillus fumigatus (∼106 spores/egg), and 2 Escherichia coli (∼108 CFU/egg) isolates. Challenge (100 μL of PM or EH) was administered using a sterile loop to a 28 mm area on the blunt end of the eggshell at day 19 of embryogenesis (DOE). In 3 experiments, microbiological data were collected from environmental hatcher samples (open-agar plate method), fluff samples, postmortem whole-body chick rinse samples, and gastrointestinal tract (GIT) samples to evaluate select bacteria and fungi circulating within the hatch cabinet and colonization of GIT. Cumulative bacterial and fungal recovery from the PM hatching environment from DOE20 to hatch was higher than the nonchallenged group (NC) and EH group at ∼860 and ∼1,730 CFU, respectively. Bacterial recovery from GIT, fluff, and chick rinse samples were similar for the PM and EH group in Exp. 1. However, Aspergillus fumigatus recovery from fluff and chick rinse samples for the PM group was significantly (P < 0.001) higher than the NC and EH group. In Exp. 2 and 3, PM challenge significantly (P < 0.05) increased Gram-negative bacterial recovery from the GIT, fluff and chick rinse samples compared to both the NC and EH group. These data suggest this innovative multispecies environmental contamination model using PM could be utilized to evaluate strategies to mitigate microbial contamination in commercial hatch cabinets in a laboratory setting.

A Highly Scalable Approach to Perform Ecological Surveys of Selfing &lt;em&gt;Caenorhabditis&lt;/em&gt; Nematodes

Caenorhabditis elegans is one of the major model organisms in biology, but only recently have researchers focused on its natural ecology. The relative sparsity of information about C. elegans in its natural context comes from the challenges involved in the identification of the small nematode in nature. Despite these challenges, an increasing focus on the ecology of C. elegans has caused a wealth of new information regarding its life outside of the laboratory. The intensified search for C. elegans in nature has contributed to the discovery of many new Caenorhabditis species and revealed that congeneric nematodes frequently cohabitate in the wild, where they feed on microbial blooms associated with rotting plant material. The identification of new species has also revealed that the androdioecious mating system of males and self-fertilizing hermaphrodites has evolved three times independently within Caenorhabditis. The other two selfing species, C. briggsae and C. tropicalis, share the experimental advantages of C. elegans and have enabled comparative studies into the mechanistic basis of important traits, including self-fertilization. Despite these advances, much remains to be learned about the ecology and natural diversity of these important species. For example, we still lack functional information for many of their genes, which might only be attained through an understanding of their natural ecology. To facilitate ecological research of selfing Caenorhabditis nematodes, we developed a highly scalable method to collect nematodes from the wild. Our method makes use of mobile data collection platforms, cloud-based databases, and the R software environment to enhance researchers' ability to collect nematodes from the wild, record associated ecological data, and identify wild nematodes using molecular barcodes.

A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes.

Caenorhabditis elegans is one of the major model organisms in biology, but only recently have researchers focused on its natural ecology. The relative sparsity of information about C. elegans in its natural context comes from the challenges involved in the identification of the small nematode in nature. Despite these challenges, an increasing focus on the ecology of C. elegans has caused a wealth of new information regarding its life outside of the laboratory. The intensified search for C. elegans in nature has contributed to the discovery of many new Caenorhabditis species and revealed that congeneric nematodes frequently cohabitate in the wild, where they feed on microbial blooms associated with rotting plant material. The identification of new species has also revealed that the androdioecious mating system of males and self-fertilizing hermaphrodites has evolved three times independently within Caenorhabditis. The other two selfing species, C. briggsae and C. tropicalis, share the experimental advantages of C. elegans and have enabled comparative studies into the mechanistic basis of important traits, including self-fertilization. Despite these advances, much remains to be learned about the ecology and natural diversity of these important species. For example, we still lack functional information for many of their genes, which might only be attained through an understanding of their natural ecology. To facilitate ecological research of selfing Caenorhabditis nematodes, we developed a highly scalable method to collect nematodes from the wild. Our method makes use of mobile data collection platforms, cloud-based databases, and the R software environment to enhance researchers' ability to collect nematodes from the wild, record associated ecological data, and identify wild nematodes using molecular barcodes.

Changes in light absorption and composition of chromophoric marine-dissolved organic matter across a microbial bloom.

Marine chromophoric dissolved organic matter (m-CDOM) mediates many vital photochemical processes at the ocean's surface. Isolating m-CDOM within the chemical complexity of marine dissolved organic matter has remained an analytical challenge. The SeaSCAPE campaign, a large-scale mesocosm experiment, provided a unique opportunity to probe the in situ production of m-CDOM across phytoplankton and microbial blooms. Results from mass spectrometry coupled with UV-VIS spectroscopy reveal production of a chemodiverse set of compounds well-correlated with increases in absorbance after a bacterial bloom, indicative of autochthonous m-CDOM production. Notably, many of the absorbing compounds were found to be enriched in nitrogen, which may be essential to chromophore function. From these results, quinoids, porphyrins, flavones, and amide-like compounds were identified via structural analysis and may serve as important photosensitizers in the marine boundary layer. Overall, this study demonstrates a step forward in identifying and characterizing m-CDOM using temporal mesocosm data and integrated UV-VIS spectroscopy and mass spectrometry analyses.

The Interplay between Cs and K in Pseudanabaena Catenate; from Microbial Bloom Control Strategies to Bioremediation Options for Radioactive Waters

The Interplay between Cs and K in Pseudanabaena Catenate; from Microbial Bloom Control Strategies to Bioremediation Options for Radioactive Waters

Lethal microbial blooms delayed freshwater ecosystem recovery following the end-Permian extinction

Harmful algal and bacterial blooms linked to deforestation, soil loss and global warming are increasingly frequent in lakes and rivers. We demonstrate that climate changes and deforestation can drive recurrent microbial blooms, inhibiting the recovery of freshwater ecosystems for hundreds of millennia. From the stratigraphic successions of the Sydney Basin, Australia, our fossil, sedimentary and geochemical data reveal bloom events following forest ecosystem collapse during the most severe mass extinction in Earth’s history, the end-Permian event (EPE; c. 252.2 Ma). Microbial communities proliferated in lowland fresh and brackish waterbodies, with algal concentrations typical of modern blooms. These initiated before any trace of post-extinction recovery vegetation but recurred episodically for >100 kyrs. During the following 3 Myrs, algae and bacteria thrived within short-lived, poorly-oxygenated, and likely toxic lakes and rivers. Comparisons to global deep-time records indicate that microbial blooms are persistent freshwater ecological stressors during warming-driven extinction events.

Multi-kingdom ecological drivers of microbiota assembly in preterm infants.

The preterm infant gut microbiota develops remarkably predictably1–7, with pioneer species colonizing after birth, followed by an ordered succession of microbes. The gut microbiota is vital to preterm infant health8,9 yet the forces underlying these predictable dynamics remain unknown. The environment, the host, and microbe-microbe interactions are all likely to shape microbiota dynamics, but in such a complex ecosystem identifying the specific role of any individual factor has remained a major challenge10–14. Here we use multi-kingdom absolute abundance quantitation, ecological modelling, and experimental validation to overcome this challenge. We quantify the absolute bacterial, fungal, and archaeal dynamics in a longitudinal cohort of 178 preterm infants. We uncover, with exquisite precision, microbial blooms and extinctions and reveal an inverse correlation between bacterial and fungal loads in the infant gut. We infer computationally and demonstrate experimentally in vitro and in vivo that predictable assembly dynamics may be driven by directed, context-dependent interactions between specific microbes. Mirroring the dynamics of macroscopic ecosystems15–17, a late-arriving member, Klebsiella, exploits the pioneer, Staphylococcus, to gain a foothold within the gut. Remarkably, we find that interactions between kingdoms can influence assembly, with a single fungal species, Candida albicans, inhibiting multiple dominant gut bacteria. Our work unveils the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, critical for both our understanding of microbiota ecology and targeted microbiota interventions.

The Role of Dietary Fibre in Modulating Gut Microbiota Dysbiosis in Patients with Type 2 Diabetes: A Systematic Review and Meta-Analysis of Randomised Controlled Trials.

Background: The prevalence of type 2 diabetes is on the increase worldwide, and it represents about 90% of adults who are diagnosed with diabetes. Overweight and obesity, lifestyle, genetic predisposition and gut microbiota dysbiosis have been implicated as possible risk factors in the development of type 2 diabetes. In particular, low intake of dietary fibre and consumption of foods high in fat and sugar, which are common in western lifestyle, have been reported to contribute to the depletion of specific bacterial taxa. Therefore, it is possible that intake of high dietary fibre may alter the environment in the gut and provide the needed substrate for microbial bloom. Aim: The current review is a systematic review and meta-analysis which evaluated the role of dietary fibre in modulating gut microbiota dysbiosis in patients with type 2 diabetes. Methods: This is a systematic review and meta-analysis of randomised controlled trials which relied on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework. Electronic searches were conducted using EBSCOHost with links to Health Sciences Research Databases, EMBASE and Google Scholar. The reference lists of articles were also searched for relevant studies. Searches were conducted from date of commencement of the database to 5 August 2020. The search strategy was based on the Population, Intervention, Comparator, Outcomes, Studies (PICOS) framework and involved the use of synonyms and medical subject headings (MesH). Search terms were combined with Boolean operators (OR/AND). Results: Nine studies which met the inclusion criteria were selected for the systematic review and meta-analysis, and four distinct areas were identified: the effect of dietary fibre on gut microbiota; the role of dietary fibre on short-chain fatty acids (SCFAs); glycaemic control; and adverse events. There was significant difference (p < 0.01) in the relative abundance of Bifidobacterium with a mean difference of 0.72 (95% CI, 0.56, 0.89) between the dietary fibre group compared with placebo. In relation to the meta-analysis for SCFAs, while there was significant difference (p = 0.02) between the dietary fibre group and placebo with a standardised mean difference of 0.5 (95% CI, 0.08, 0.91) regarding total SCFAs, the differences were not significant (p > 0.05) in relation to acetic acid, propionic acid and butyric acid. There was only significant improvement (p = 0.002) with respect to glycated haemoglobin with a mean difference of −0.18 (95% CI, −0.29, −0.06) between the dietary fibre group and placebo group. Differences between the two groups were not significant (p > 0.05) in relation to fasting blood glucose and homeostatic model assessment of insulin resistance (HOMA-IR). Furthermore, there were no significant differences between the two groups in subjects who reported adverse events. It is possible that the promotion of SCFA producers in greater diversity and abundance by dietary fibre in this review led to improvement in glycated haemoglobin, partly due to increased glucagon-like peptide-1 (GLP-1) production. In addition, Bifidobacterium lactis has been reported to increase glycogen synthesis, decrease expression of hepatic gluconeogenesis genes, improve translocation of glucose transport-4 and promote glucose uptake. It is also possible that the reduction in body weight of participants in the intervention group compared with control may have contributed to the observed improvement in glycated haemoglobin. Conclusion: This systematic review and meta-analysis have demonstrated that dietary fibre can significantly improve (p < 0.05) the relative abundance of Bifidobacterium, total SCFAs and glycated haemoglobin. However, dietary fibre did not appear to have significant effect (p > 0.05) on fasting blood glucose, HOMA-IR, acetic acid, propionic acid, butyric acid and adverse events.