Earth's Biomass Research Articles

Polysaccharide breakdown products drive degradation-dispersal cycles of foraging bacteria through changes in metabolism and motility.

Most of Earth's biomass is composed of polysaccharides. During biomass decomposition, polysaccharides are degraded by heterotrophic bacteria as a nutrient and energy source and are thereby partly remineralized into CO2. As polysaccharides are heterogeneously distributed in nature, following the colonization and degradation of a polysaccharide hotspot the cells need to reach new polysaccharide hotspots. Even though many studies indicate that these degradation-dispersal cycles contribute to the carbon flow in marine systems, we know little about how cells alternate between polysaccharide degradation and motility, and which environmental factors trigger this behavioral switch. Here, we studied the growth of the marine bacterium Vibrio cyclitrophicus ZF270 on the abundant marine polysaccharide alginate, both in its soluble polymeric form as well as on its breakdown products. We used microfluidics coupled to time-lapse microscopy to analyze motility and growth of individual cells, and RNA sequencing to study associated changes in gene expression. We found that single cells grow at reduced rate on alginate until they form large groups that cooperatively break down the polymer. Exposing cell groups to digested alginate accelerates cell growth and changes the expression of genes involved in alginate degradation and catabolism, central metabolism, ribosomal biosynthesis, and transport. However, exposure to digested alginate also triggers cells to become motile and disperse from cell groups, proportionally increasing with the group size before the nutrient switch, and this is accompanied by high expression of genes involved in flagellar assembly, chemotaxis, and quorum sensing. The motile cells chemotax toward polymeric but not digested alginate, likely enabling them to find new polysaccharide hotspots. Overall, our findings reveal cellular mechanisms that might also underlie bacterial degradation-dispersal cycles, which influence the remineralization of biomass in marine environments.

Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life.

Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.

Recent Advances in Biomedical Nanotechnology Related to Natural Products.

Natural product processing via nanotechnology has opened the door to innovative and significant applications in medical fields. On one hand, plants-derived bioactive ingredients such as phenols, pentacyclic triterpenes and flavonoids exhibit significant pharmacological activities, on another hand, most of them are hydrophobic in nature, posing challenges to their use. To overcome this issue, nanoencapsulation technology is employed to encapsulate these lipophilic compounds and enhance their bioavailability. In this regard, various nano-sized vehicles, including degradable functional polymer organic compounds, mesoporous silicon or carbon materials, offer superior stability and retention for bioactive ingredients against decomposition and loss during delivery as well as sustained release. On the other hand, some naturally occurring polymers, lipids and even microorganisms, which constitute a significant portion of Earth's biomass, show promising potential for biomedical applications as well. Through nano-processing, these natural products can be developed into nano-delivery systems with desirable characteristics for encapsulation a wide range of bioactive components and therapeutic agents, facilitating in vivo drug transport. Beyond the presentation of the most recent nanoencapsulation and nano-processing advancements with formulations mainly based on natural products, this review emphasizes the importance of their physicochemical properties at the nanoscale and their potential in disease therapy.

The Hidden Hydrogeosphere: The Contribution of Deep Groundwater to the Planetary Water Cycle

The canonical water cycle assumes that all water entering the subsurface to form groundwater eventually reenters the surface water cycle by discharge to lakes, streams, and oceans. Recent discoveries in groundwater dating have challenged that understanding. Here we introduce a new conceptual framework that includes the large volume of water that is estimated to account for 30–46% of the planet's groundwater but that is not yet incorporated in the traditional water cycle. This immense hidden hydrogeosphere has been overlooked to date largely because it is stored deeper in the crust, on long timescales ranging from tens of thousands to more than one billion years. Here we demonstrate why understanding of this deep, old groundwater is critical to society's energy, resource, and climate challenges as the deep hydrogeosphere is an important target for exploration for new resources of helium, hydrogen, and other elements critical to the green energy transition; is under investigation for geologic repositories for nuclear waste and for carbon sequestration; and is the biome for a deep subsurface biosphere estimated to account for a significant proportion of Earth's biomass. ▪We provide a new conceptual framework for the hidden hydrogeosphere, the 30–46% of groundwater previously unrecognized in canonical water cycles.▪Geochemico-statistical modeling groundwater age distributions allows deconvolution of timing, rates, and magnitudes of key crustal processes.▪Understanding and modeling this deep, old groundwater are critical to addressing society's energy, resource, and climate challenges.

A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

The greening ashore.

More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.

Mikroplastik sebagai Kontaminan Anyar dan Efek Toksiknya terhadap Kesehatan

Microplastics are synthetic polymers that are unable to be completely degraded and will stay as an environmental contaminant for a long period of time. Due to their microscopic size, microplastics are able to enter the human body, either directly or indirectly via the food chain, where both processes will induce pathological changes in-vivo. So far, clinically, there has been no direct evidence yet about any microplastic-related disease in humans. However, since Indonesia is a maritime country and has been producing microplastics on a large scale, it is critical for our healthcare personnel to have the knowledge about microplastic toxicokinetics and the possible pathological responses elicited by humans when exposed to microplastics. This review article aims to discuss the definition, genesis, accumulation process, toxicokinetics, and pathological responses due to microplastic exposure, emphasizing the biomolecular aspects and implying the possible effects on public health. An internet search in Google Scholar and Pubmed was performed using keywords "microplastics" and "health", as well as their Indonesian language counterparts. Full-text English or Indonesian text from the year 2018 to 2020 were gathered and used as the primary references for this literature review. Microplastics are a novel emerging contaminant that is currently accumulating in the earth's biomass with the potency to induce pathological changes in the human body. Health practitioners are expected to have knowledge about the harm of microplastic to humans. Eventually, follow-up acts should be taken to prevent and manage the microplastic-related pathologies as discussed further in this review.

Botanical priming helps overcome plant blindness on a memory task

Humans often fail to notice plants in the environment and our plant blindness leads to an inability to prioritise plants equally to other living categories such as animals. Evidence for plant blindnesss comes from memory tasks presenting pictures of single items where adults recall fewer plant than animal images. However, it remains unknown as to whether plant blindness affects recall of elements in complex scenarios and whether the effects can be attenuated. In Experiment 1, we uncovered that plant blindness biases adults' performance in a memory task where plant elements were presented simultaneously and saliently alongside animal elements in naturalistic scenes. In Experiment 2, priming adults with words about plants dominating the Earth's biomass did not attenuate plant-animal differentials on the memory task. In Experiment 3, adults recalled plants just as well as animals after being primed by task-relevant pictures of a tree. These results suggest that plant blindness is a visual bias that can impact the way adults process real-world scenes, but it can also be corrected by a perceptual form of priming.

An overview of the ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) project: aerosol–cloud–radiation interactions in the southeast Atlantic basin

Abstract. Southern Africa produces almost a third of the Earth's biomass burning (BB) aerosol particles, yet the fate of these particles and their influence on regional and global climate is poorly understood. ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) is a 5-year NASA EVS-2 (Earth Venture Suborbital-2) investigation with three intensive observation periods designed to study key atmospheric processes that determine the climate impacts of these aerosols. During the Southern Hemisphere winter and spring (June–October), aerosol particles reaching 3–5 km in altitude are transported westward over the southeast Atlantic, where they interact with one of the largest subtropical stratocumulus (Sc) cloud decks in the world. The representation of these interactions in climate models remains highly uncertain in part due to a scarcity of observational constraints on aerosol and cloud properties, as well as due to the parameterized treatment of physical processes. Three ORACLES deployments by the NASA P-3 aircraft in September 2016, August 2017, and October 2018 (totaling ∼350 science flight hours), augmented by the deployment of the NASA ER-2 aircraft for remote sensing in September 2016 (totaling ∼100 science flight hours), were intended to help fill this observational gap. ORACLES focuses on three fundamental science themes centered on the climate effects of African BB aerosols: (a) direct aerosol radiative effects, (b) effects of aerosol absorption on atmospheric circulation and clouds, and (c) aerosol–cloud microphysical interactions. This paper summarizes the ORACLES science objectives, describes the project implementation, provides an overview of the flights and measurements in each deployment, and highlights the integrative modeling efforts from cloud to global scales to address science objectives. Significant new findings on the vertical structure of BB aerosol physical and chemical properties, chemical aging, cloud condensation nuclei, rain and precipitation statistics, and aerosol indirect effects are emphasized, but their detailed descriptions are the subject of separate publications. The main purpose of this paper is to familiarize the broader scientific community with the ORACLES project and the dataset it produced.

Microbial Life in Impact Craters.

Asteroid and comet impacts are known to have caused profound disruption to multicellular life, yet their influence on habitats for microorganisms, which comprise the majority of Earth's biomass, is less well understood. Of particular interest are geological changes in the target lithology at and near the point of impact that can persist for billions of years. Deep subsurface and surface-dwelling microorganisms are shown to gain advantages from impact-induced fracturing of rocks. Deleterious changes are associated with impact-induced closure of pore spaces in rocks. Superimposed on these long-term geological changes are post-impact alterations such as changes in the hydrological system in and around a crater. The close coupling between geological changes and the conditions for microorganisms yields a synthesis of the fields of microbiology and impact cratering. We use these data to discuss how craters can be used in the search for life beyond Earth.

A Maximum Subsurface Biomass on Mars from Untapped Free Energy: CO and H2 as Potential Antibiosignatures.

Whether extant life exists in the martian subsurface is an open question. High concentrations of photochemically produced CO and H2 in the otherwise oxidizing martian atmosphere represent untapped sources of biologically useful free energy. These out-of-equilibrium species diffuse into the regolith, so subsurface microbes could use them as a source of energy and carbon. Indeed, CO oxidation and methanogenesis are relatively simple and evolutionarily ancient metabolisms on Earth. Consequently, assuming CO- or H2-consuming metabolisms would evolve on Mars, the persistence of CO and H2 in the martian atmosphere sets limits on subsurface metabolic activity. In this study, we constrain such maximum subsurface metabolic activity on Mars using a one-dimensional photochemical model with a hypothetical global biological sink on atmospheric CO and H2. We increase the biological sink until the modeled atmospheric composition diverges from observed abundances. We find maximum biological downward subsurface sinks of 1.5 × 108 molecules/(cm2·s) for CO and 1.9 × 108 molecules/(cm2·s1) for H2. These convert to a maximum metabolizing biomass of ≲1027 cells or ≤2 × 1011 kg, equivalent to ≤10-4-10-5 of Earth's biomass, depending on the terrestrial estimate. Diffusion calculations suggest that this upper biomass limit applies to the top few kilometers of the martian crust in communication with the atmosphere at low to mid-latitudes. This biomass limit is more robust than previous estimates because we test multiple possible chemoautotrophic ecosystems over a broad parameter space of tunable model variables using an updated photochemical model with precise atmospheric concentrations and uncertainties from Curiosity. Our results of sparse or absent life in the martian subsurface also demonstrate how the atmospheric redox pairs of CO-O2 and H2-O2 may constitute antibiosignatures, which may be relevant to excluding life on exoplanets.

Desert Dust, Industrialization, and Agricultural Fires: Health Impacts of Outdoor Air Pollution in Africa

AbstractThe African continent continuously experiences extreme aerosol load conditions, during which the World Health Organization clean air standard of 10 μg/m3 of PM2.5 mass is systematically exceeded. Africa holds the world largest source of desert dust emissions, undergoes strong industrial growth, and produces approximately a third of the Earth's biomass burning aerosol particles. Sub‐Saharan biomass burning is driven by agricultural practices, such as burning fields and bushes in the postharvest season for fertilization, land management, and pest control. Thus, these emissions are predominantly anthropogenic. Here we use global atmospheric composition, climate, and health models to simulate the chemical composition of the atmosphere and calculate the mortality rates for Africa by distinguishing between purely natural, industrial/domestic, and biomass burning emissions. Air quality‐related deaths in Africa rank within the top leading causes of death in Africa. Our results of ~780,000 premature deaths annually point to the extensive health impacts of natural emissions, high mortality rate caused by industrialization in Nigeria and South Africa, and a smaller extent by fire emissions in Central and West Africa. In Africa, 43,000 premature deaths are linked to biomass burning mainly driven by agriculture. Our results also show that natural sources, in particular windblown dust emissions, have large impacts on air quality and human health in Africa.

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.

The deep terrestrial biosphere harbours a substantial fraction of Earth's biomass and remains understudied compared with other ecosystems. Deep biosphere life primarily consists of bacteria and archaea, yet knowledge of their co-occurring viruses is poor. Here, we temporally catalogued viral diversity from five deep terrestrial subsurface locations (hydraulically fractured wells), examined virus-host interaction dynamics and experimentally assessed metabolites from cell lysis to better understand viral roles in this ecosystem. We uncovered high viral diversity, rivalling that of peatland soil ecosystems, despite low host diversity. Many viral operational taxonomic units were predicted to infect Halanaerobium, the dominant microorganism in these ecosystems. Examination of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) spacers elucidated lineage-specific virus-host dynamics suggesting active in situ viral predation of Halanaerobium. These dynamics indicate repeated viral encounters and changing viral host range across temporally and geographically distinct shale formations. Laboratory experiments showed that prophage-induced Halanaerobium lysis releases intracellular metabolites that can sustain key fermentative metabolisms, supporting the persistence of microorganisms in this ecosystem. Together, these findings suggest that diverse and active viral populations play critical roles in driving strain-level microbial community development and resource turnover within this deep terrestrial subsurface ecosystem.

The deep history of Earth's biomass

The subsurface ‘deep biosphere’ represents one-tenth to one-third of Earth's total global present-day biomass. The rest is dominated by land plants, a relatively recent development in geological history. Before c. 400 Ma, a relatively low surface biomass with high productivity and fast turnover supplied carbon to a deep biosphere with high biomass but low productivity and slow turnover. Here, we argue that the deep biosphere outweighed the surface biosphere by about one order of magnitude for at least half of the history of life on Earth. This result offers a new perspective on the history of life on Earth with important implications for the search for life on other worlds.

Characterizing the Deep Terrestrial Subsurface Microbiome.

A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.

Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses.

Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.

Using Metagenomics to Connect Microbial Community Biodiversity and Functions.

Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.

CO2 and carbonate as substrate for the activation of the microbial community in 180 m deep bedrock fracture fluid of Outokumpu Deep Drill Hole, Finland.

Microbial communities in deep subsurface environments comprise a large portion of Earth's biomass, but the metabolic activities in these habitats are largely unknown. Here the effect of CO2 and carbonate on the microbial community of an isolated groundwater fracture zone at 180 m depth of the Outokumpu Deep Scientific Drill Hole (Finland) was tested. Outokumpu groundwater at 180 m depth contains approximately 0.45 L L−1 dissolved gas of which methane contributes 76%. CO2, on the other hand, is scarce. The number of microbial cells with intracellular activity in the groundwater was low when examined with redox staining. Fluorescence Assisted Cell Sorting (FACS) analyses indicated that only 1% of the microbial community stained active with the redox sensing dye in the untreated groundwater after 4 weeks of starvation. However, carbon substrate and sulfate addition increased the abundance of fluorescent cells up to 7%. CO2 and CO2 + sulfate activated the greatest number of microbes, especially increasing the abundance of Pseudomonas sp., which otherwise was present at only low abundance in Outokumpu. Over longer exposure time (2 months) up to 50% of the bacterial cells in the groundwater were shown to incorporate inorganic carbon from carbonate into biomass. Carbon recapture is an important feature in this ecosystem since it may decrease the rate of carbon loss in form of CO2 released from cellular processes.

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow ‘modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, ‘old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Diversity of phosphorus reserves in microorganisms.

Phosphorus compounds are indispensable components of the Earth's biomass metabolized by all living organisms. Under excess of phosphorus compounds in the environment, microorganisms accumulate reserve phosphorus compounds that are used under phosphorus limitation. These compounds vary in their structure and also perform structural and regulatory functions in microbial cells. The most common phosphorus reserve in microorganism is inorganic polyphosphates, but in some archae and bacteria insoluble magnesium phosphate plays this role. Some yeasts produce phosphomannan as a phosphorus reserve. This review covers also other topics, i.e. accumulation of phosphorus reserves under nutrient limitation, phosphorus reserves in activated sludge, mycorrhiza, and the role of mineral phosphorus compounds in mammals.