Marine DNA exposes massive gaps in ocean biosphere maps and finds fish in unexpected places

What little we still know about our oceans! And this study seems to have focused primarily on small fish (what about bigger fish?).

This is one reason among others whey global warming/climate change is a hoax!

"... The problem with current mapping projects, which aim to chart where species live and the conditions they need to survive, is that they are based on limited information. Traditional methods such as nets and underwater cameras primarily target easy-to-reach areas and often miss small, elusive species. This means our picture of ocean biodiversity is far from complete. ...

To fill these knowledge gaps, research ... used a powerful technique called Environmental DNA (eDNA). This approach can detect multiple species and identify their ranges without capturing or photographing them.

The research team collected nearly 1,000 water samples from 542 locations worldwide, including polar regions and tropical islands. They then analyzed the fish DNA in those samples and compared it with occurrence databases, such as the Global Biodiversity Information Facility (GBIF).

These new eDNA surveys reveal just how incomplete our records are. According to results published by the team in PLOS Biology, 93% of geographic ranges were underestimated. This means species were living far outside the areas where they were historically mapped. For example, the crocodile icefish, which was previously known only to live in the freezing conditions of the Antarctic region, was detected in Patagonia (southern South America).

Additionally, 7% of species' ecological niches were also underestimated, meaning they were found to tolerate environmental conditions that were previously thought impossible for them to live. ...

The clear implication of these findings is that current mapping methods need to be updated, as they leave vast blind spots. ..."

From the abstract:

"Assessing species geographic distributions is critical to approximate their ecological niches, understand how global change may reshape their occurrence patterns, and predict their extinction risks. Yet, species records are over-aggregated across taxonomic, geographic, environmental, and anthropogenic dimensions.

The under-sampling of remote locations biases the quantification of species geographic distributions and ecological niche for most species.

Here, we used nearly one thousand environmental DNA (eDNA) samples across the world’s oceans, including polar regions and tropical remote islands, to determine the extent to which the geographic and ecological niche ranges of marine fishes are underestimated through the lens of global occurrence records based on conventional surveys.

Our eDNA surveys revealed that the known geographic ranges for 93% of species and the ecological niche ranges for 7% of species were underestimated, and contributed to filling them.

We show that the probability to detect a range filling for a given species is primarily shaped by the GBIF/OBIS sampling effort in a cell, but also by the number of occurrences available for the species. Most gap fillings were achieved by addressing a methodological sampling bias, notably when eDNA facilitated the detection of small fishes in previously sampled locations using conventional methods.

Using a machine learning model, we found that a local effort of 10 eDNA samples would detect 24 additional fish species on average and a maximum of 98 species in previously unsampled tropical areas. Yet, a null model revealed that only half of ecological niche range fillings would be due to eDNA surveys, beyond a random allocation of classical sampling effort. Altogether, our results suggest that sampling in remote areas and performing eDNA surveys in over-sampled areas may both increase fish ecological niche ranges toward unexpected values with consequences in biodiversity modeling, management, and conservation."

Marine DNA exposes massive gaps in ocean maps and finds fish in unexpected places

eDNA surveys substantially expand known geographic and ecological niche boundaries of marine fishes (open access)

Fig 1. Map of both GBIF/OBIS and eDNA surveys, and the distribution of their associated environmental and anthropogenic variables.

Fig 2. Map of the predicted number of fish species gained in a cell if 10 eDNA samples were added to GBIF/OBIS sampling records, if any.

Bacteria ‘breathed’ oxygen nearly a billion years before the Great Oxidation Event

Amazing stuff!

"Aerobic respiration—using oxygen to power the process of producing cellular fuel—was a huge development for life on Earth. After some microbes figured out photosynthesis, levels of oxygen in the atmosphere jumped dramatically, resulting in what’s commonly called the Great Oxygenation Event some 2.3 billion years ago, paving the way for oxygen-breathing life to take over. But it’s never been clear when the ability to metabolize oxygen evolved. Now, thanks to a combination of fossil, genetic, and geological data, researchers have a new estimate— and it’s 900 million years before photosynthesis pumped oxygen into the atmosphere. 

..."

From the editor's summary and abstract:

"Editor’s summary

When exploring deep time, the problem is that there are few, if any, good fossils of the earliest living organisms, and it is impossible to precisely date the evolution of those that do exist.

One calibration point is provided by the impact event about 4.5 billion years ago that resulted in sterilization of Earth and formation of the Moon. Davín et al. used molecular clocks, machine learning, and phylogenetic reconciliation to present a reconstruction of the evolution of Earth’s bacterial biosphere over the past 4 billion years with particular emphasis on aerobic metabolisms. Their analysis showed that the last common ancestor of bacteria likely existed 4.4 to 3.9 billion years ago, and aerobic organisms likely emerged before the Great Oxidation Event (2.43 to 2.33 billion years ago). Oxygen tolerance may have been a prerequisite for, rather than a consequence of, the evolution of oxygenic photosynthesis. ...

Structured Abstract

INTRODUCTION

Microbial life dominates the biosphere, but a timescale of early microbial evolution has proven elusive as a result of an inadequate fossil record. The lack of maximum age calibrations—the earliest point in time at which a given group might have emerged—is particularly problematic.

However, the geochemical record bears the imprint of microbial metabolism through time, providing a complementary source of information.

A pivotal event in this history was the Great Oxidation Event (GOE) ~2.43 to 2.33 billion years ago (Ga), which marked a substantial increase in atmospheric oxygen.

This transition, driven by the evolution of cyanobacterial oxygenic photosynthesis and carbon burial, transformed the biosphere from predominantly anoxic to oxic, causing widespread adaptation to oxygen. In this study, we used the temporal link between atmospheric oxygenation and the evolutionary spread of aerobic metabolism to calibrate the phylogeny of the bacterial domain.

RATIONALE

To date the bacterial tree, we introduced multiple new maximum age calibrations by linking the GOE to the age of aerobic lineages. We used a Bayesian approach that assumes that aerobic nodes are unlikely to be older than the GOE but can predate it given sufficient evidence from fossils or sequence divergence. To implement this approach, we integrated phylogenetic reconciliation with machine learning to map transitions from anaerobic to aerobic lifestyles onto the bacterial tree. By aggregating signals across the genome, we could robustly infer aerobic and anaerobic phenotypes from incomplete ancestral gene repertoires.

RESULTS

We identified 84 anaerobic to aerobic transitions on a species tree of 1007 bacteria. Most transitions occurred after the GOE and were driven by horizontal acquisition of respiratory and oxygen tolerance genes.

However, despite the GOE calibration, at least three transitions predated this event, suggesting that aerobic respiration evolved before widespread atmospheric oxygenation and may have facilitated the evolution of oxygenic photosynthesis in cyanobacteria.

Our molecular clock analyses estimated that the last bacterial common ancestor lived in the Hadean or earliest Archaean era (4.4 to 3.9 Ga), whereas bacterial phyla originated in the Archaean and Proterozoic eras (2.5 to 1.8 Ga); most bacterial families are as old as land plants and animal phyla, dating back to the late Proterozoic (0.6 to 0.75 Ga).

CONCLUSION

We infer that the earliest aerobic bacteria emerged in the Archaean, predating the GOE by 900 million years. After the GOE, aerobic lineages experienced faster diversification than their anaerobic counterparts, highlighting the impact of atmospheric oxygenation on bacterial evolution. The approach developed here provides a framework for linking microbial traits to Earth’s geochemical history, offering a pathway for exploring the evolution of other phenotypes in the context of Earth’s history."

ScienceAdviser

A geological timescale for bacterial evolution and oxygen adaptation

An integrated approach to date bacterial evolution and reconstruct the history of oxygen adaptation.

Tons of life deep below the land surfaces and seafloor surfaces of the Earth

Amazing stuff! What little do we still know about life on Earth!

"Barely living "zombie" bacteria and other forms of life constitute an immense amount of carbon deep within Earth's subsurface - 245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth's innermost secrets. ..."

"... Researchers compared more than 1000 samples from 50 marine and terrestrial ecosystems and found that, true to prior beliefs, the deeper you dig on land, the lower the diversity of life. But under the seafloor, all bets are off. Samples from nearly 500 meters below the bottom of the ocean were full of weird microbes. “We show that in some subsurface environments, the diversity can easily rival, if not exceed, diversity at the surface,”  ... “We can now appreciate that perhaps half the microbial diversity on Earth is in the subsurface." ..."

"Which microbes thrive below us in darkness – in gold mines, in aquifers, in deep boreholes in the seafloor – and how do they compare to the microbiomes that envelop the Earth’s surfaces, on land and sea?

The first global study to embrace this huge question, conducted at the Marine Biological Laboratory (MBL), Woods Hole, reveals astonishingly high microbial diversity in some subsurface environments (up to 491 meters below the seafloor and up to 4375 m below ground). ..."

From the abstract:

"Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth’s subsurface and surface environments."

ScienceAdviser

Life in deep Earth totals 15 to 23 billion tons of carbon -- hundreds of times more than humans "Deep Carbon Observatory collaborators, exploring the 'Galapagos of the deep,' add to what's known, unknown, and unknowable about Earth's most pristine ecosystem"

Living in the deep, dark, slow lane: Insights from the first global appraisal of microbiomes in earth’s subsurface environments

Living in the Deep, Dark, Slow Lane (original news release) "Insights from the First Global Appraisal of Life Below the Earth's Surface"

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide (open access)

Fig. 2. Microbial diversity in marine and terrestrial biome.

A team of geomicrobiologists walking to a sampling site at the end of an inactive tunnel in a South African gold mine. At this site almost 3 km deep beneath the surface, the researchers can access one of the deepest and oldest ecosystems on Earth. The brines in which these microbes live have been trapped in the rock for more than 1 billion years. 

Bacteria from a Coal Bed 2 Km below the Pacific Ocean Floor off Japan

Higher than expected CO2 fertilization inferred from leaf to global observations

More evidence that Global Warming (aka climate change) is a hoax!

This is not the first scientific research confirming that the higher CO2 concentration in the air leads to more greening and more photosynthesis absorbing CO2. I bet you this is poorly reflected in climate models!

"Several lines of evidence point to an increase in the activity of the terrestrial biosphere over recent decades, impacting the global net land carbon sink (NLS) and its control on the growth of atmospheric carbon dioxide (ca ). Global terrestrial gross primary production (GPP)—the rate of carbon fixation by photosynthesis—is estimated to have risen by (31 ± 5)% since 1900, but the relative contributions of different putative drivers to this increase are not well known. Here we identify the rising atmospheric CO2 concentration as the dominant driver. ... These findings suggest a larger beneficial role of the land carbon sink in modulating future excess anthropogenic CO2 ... Four independent lines of evidence indicate intensifying terrestrial biosphere activity ... "

Higher than expected CO2 fertilization inferred from leaf to global observations - Haverd - 2020 - Global Change Biology - Wiley Online Library