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  • 400-300 mya
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        • Springtails
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    • 360-300mya Carboniferous
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  • 300-200 mya
  • 200-100 mya
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Soil Evolution
  • Home
    • Start
      • Soil & Civilisation
      • Seeing Soil
      • Soil Science
      • New Science
      • Short story
    • What is Soil?
      • Clay
      • Soil Structure
      • Biome
      • Glomalisation
        • Testing
      • Soil Functions
        • Energy
          • Entropy
      • Decomposition
        • Mineralisation
        • De-lignification
        • Humification
      • Types
        • Europe
    • Challenge
      • Terrestrialisation
      • Theories so far
      • Tools
    • Darwin's version
    • Timeline
      • Copy of 100mya - 0 mya
      • Copy of 200-100 mya
      • Copy of 300-200 mya
      • Copy of 400-300 mya
      • Copy of 500-400 mya
  • 500-400 mya
    • No Soil
    • 4.500 - 1000 mya
    • 1000 - 500 mya
    • Periods
      • Cambrian
      • Ordovician
      • Silurian
    • Biology
      • Plants
      • Animals
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  • 400-300 mya
    • 400-360 mya Late Devonian
      • Green cover
      • Vascular Plants
      • Mycorrhiza (AMF)
      • Animals
        • Springtails
        • Arachnids
    • 360-300mya Carboniferous
      • Plants
        • Vascular
      • Early Soils
        • Micro-aggregation
      • Animals - Early Carb
        • Oribatids - Lower
        • Origin of Insects
      • Animals - Late Carb
      • Worms
  • 300-200 mya
  • 200-100 mya
    • 200-145 mya Jurassic
    • 145-66 mya Cretaceous
  • 100mya - 0 mya
    • 66 - 0 mya Cenozoic
  • Now
    • Present State of Soil
      • Desertification
      • Concretisation
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      • Problem
      • Biological
    • Soil & Global Warming
      • Soil Surfaces & Global Warming
      • Soil Carbon
      • Soil & Water
      • Soil Temperature
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      • Climate Change
    • Save our Soil!
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  • More
    • Home
      • Start
        • Soil & Civilisation
        • Seeing Soil
        • Soil Science
        • New Science
        • Short story
      • What is Soil?
        • Clay
        • Soil Structure
        • Biome
        • Glomalisation
          • Testing
        • Soil Functions
          • Energy
            • Entropy
        • Decomposition
          • Mineralisation
          • De-lignification
          • Humification
        • Types
          • Europe
      • Challenge
        • Terrestrialisation
        • Theories so far
        • Tools
      • Darwin's version
      • Timeline
        • Copy of 100mya - 0 mya
        • Copy of 200-100 mya
        • Copy of 300-200 mya
        • Copy of 400-300 mya
        • Copy of 500-400 mya
    • 500-400 mya
      • No Soil
      • 4.500 - 1000 mya
      • 1000 - 500 mya
      • Periods
        • Cambrian
        • Ordovician
        • Silurian
      • Biology
        • Plants
        • Animals
        • Bacteria
    • 400-300 mya
      • 400-360 mya Late Devonian
        • Green cover
        • Vascular Plants
        • Mycorrhiza (AMF)
        • Animals
          • Springtails
          • Arachnids
      • 360-300mya Carboniferous
        • Plants
          • Vascular
        • Early Soils
          • Micro-aggregation
        • Animals - Early Carb
          • Oribatids - Lower
          • Origin of Insects
        • Animals - Late Carb
        • Worms
    • 300-200 mya
    • 200-100 mya
      • 200-145 mya Jurassic
      • 145-66 mya Cretaceous
    • 100mya - 0 mya
      • 66 - 0 mya Cenozoic
    • Now
      • Present State of Soil
        • Desertification
        • Concretisation
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      • Practices affecting Soil
        • Chemical
          • Fertilisers
          • Carbon
          • Pesticides
        • Problem
        • Biological
      • Soil & Global Warming
        • Soil Surfaces & Global Warming
        • Soil Carbon
        • Soil & Water
        • Soil Temperature
        • Soil Biota
        • Climate Change
      • Save our Soil!
        • Soil Health
        • Regenerate
        • Ecology
        • Economics

Vascular Plants 

400-360 mya

Mycorrhiza Animals Springtails Arachnids Worms Green Cover

Plants

The Early Devonian saw the development of terrestrial flora. Evidence of small plants have been found in the Rhynie chert – named after the village of Rhynie in Scotland, where there is a sedimentary deposit with fabulous fossils, from around 400 mya. It seems that Rhynie is based on peat which implies that plants were growing and dying but not decomposing, leaving a large leaf litter.

Over the next few tens of millions of years, communities of simple plants, creatures, fungi and bacteria were beginning to form important relations, helping the spreading green over the surface. Spore-bearing plants took over the richest habitats, while seed plants remained in low-resource, stressful habitats.

The primitive vascular plants started to develop rhizomes (early roots) that  provided a new living environment, and their leaves fell collecting as a litter to provide ground cover adding further protection. That litter collects without being broken down.

Plants
Rhyniophytes
Trimerophytes
Earliest fossil forest
Archaeopteris
Cordaites
Rhizomes
Roots
Rhizosphere
AMF & Bacteria
Bacteria in the rhizosphere
Evolution

Phytes

Embryophytes are where the embryo is retained within maternal tissue. Living embryophytes include the bryophytes we came across over 400mya, now being joined by lycophytes, and ferns, as well as gymnosperms, like gingos and conifers.

Ferns and lycophytes are distinct lineages, the latter being the oldest lineage among existing vascular plants, and ferns the sister group to seed plants. Historically, both lineages have been studied together and treated as 'pteridophytes'. Early vascular plants are seedless, reproducing by spores and include club mosses, horsetails and ferns..

Rhyniophytes

Rhyniophytes are a group of extinct vascular land plants that flourished around 400mya (early Devonian 416–380 mya). They had short upright aerial axes (‘stems’), several centimetres tall, that arose from rhizomes or corms and branched dichotomously to form two equal growing points. The ‘naked’ branches lacked leaves and ended in multicellular spore-forming organs (sporangia). Rhyniophytes, such as Cooksonia and Rhynia (named after fossil-rich chert deposits at Rhynie (above) in Scotland), were the earliest true vascular plants,  

Trimerophytes 

Trimerophytes  are agroup of extinct land plants that flourished during 380–360 mya (late Devonian), members of which evolved into the ancestors of seed plants and ferns. They were robust herbs and small shrubs, some up to 3 m tall, and showed significant changes in branching pattern compared with their predecessors, the rhyniophytes. Instead of equal (dichotomous) branching, one stem tended to be dominant and give rise to smaller lateral branches, some bearing spore-forming organs and others acting as leaves. 

Earliest fossil forest

"Across the DFS (distributive fluvial system) there is evidence of plant-sediment interactions in the form of vegetation-induced sedimentary structures, rooting features, and accumulations of plant debris. Plant remains are also found in nearshore facies adjacent to the DFS, attesting to the development of a novel non-marine/marine teleconnection from the production and export of new biological sedimentary particles."  Davies et al 2024

What are new biological sedimentary particles?

"The sedimentary context of the plant remains sheds light on the biogeomorphic impacts of these earliest forests. The trees colonized a sizeable distributive fluvial system (DFS) that was prone to seasonal disturbance events. The nature of the sedimentary system has created a bias to those facies (character of a rock expressed by its formation, composition, and fossil content). where biogeomorphic signatures are most frequently recorded (from the distal parts of the system)." Davies et al 2024

"Calamophyton, at first glance resemble palm trees, but they were a ‘prototype’ of the kinds of trees we are familiar with today. Rather than solid wood, their trunks were thin and hollow in the centre "

Davies et al 2024

Vascular

The very primitive plants like and include algae, liverworts and mosses, are ‘non’ vascular’, in that they do not have internal systems to carry water. Their cells are not very 'differentiated' into leaves stems and roots, but are all similar.

Plants are said to be 'vascular' when they have internal water-carrying systems. These consist of tissues called xylem to transport water up, while tissue called phloem moves food downward from the leaves to roots. [CH6] Xylem is very strong to hold the water, and is the woody part – laden with ‘lignin’. This is important compound proved hard to breakdown. Phloem tissue is usually outside that and consist of starch-filled plastids.

Stems move water and nutrients to the plant's leaves and the leaves capture the sunlight the plant needs for photosynthesis These all grow in boggy conditions often on rocks/silt/water edges. They also grew some roots – and rhizomes - to take up water and nutrients and help anchor them to any cracks and crevices and accumulations of debris.

Archaeopteris

Towards the end of this period were big spore plants called Archaeopteris, that were like big ferns from a trunk. They had vascular tissue that was like wood and had formed forests of tall trees, so much so they are considered the first fossil tree.

"The scale of the root systems were really striking". The roots spread broadly from trunk, and could be ten metres in diameter. They are all quite near surface and are thought to have been preserved because they were covered in silt, not soil. The roots are similar to those of today with branches tapering, and ending as rootlets. 

Archaeopteris with very shallow roots radiating out Credit: Charles Ver Straeten

Cordaites 

Cordaites were seed-bearing plants with loose cones and strap-like leaves. They were important components of the Euramerican forests during the Late Paleozoic. There was a high diversity of cordaites in the cool temperate forests of the Russian-Siberian Platform. Some inhabited swamp-like conditions, exhibiting mangrove-like growth. This group has some affinity to modern conifers and may represent some of the earliest cone-bearing plants on Earth. 

Rhizomes

Plant rhizomes play important roles in [CH8] shaping Earth’s environments by reducing soil erosion rates and thereby increasing the stability of land surface and resilience of plant communities. Rhizomes more likely to stabilise surface – important, but not likely to grow deeply. The complex, belowground rhizome systems of a plant around this time has exposed their contribution to the formation of the earliest record of rooted red-bed soils in Asia A club moss lycopsid.appears to an immediate colonizer of any newly formed alluvium - deposit of clay, silt, and sand left by flowing floodwater. The continuous growth of a lycopsid via their rhizomes, and sequential burial in fine sediments, may have conferred erosion resistance to floodplains and contributed to the establishment of red-bed paleosols. Although these plants have limited xylem and wide cortex tissues, the rhizomatous growth of this plant could produce dense vegetation cover which would have protected the substrate against surface erosion while increasing trapping of fine particles. Perhaps more importantly, belowground rhizomes formed complex networks of aerial stems coming to ground with rhizomes, which could bind sediments in a reinforced matrix, thereby increasing soil aggregate stability (Xue et al 2016)

Roots could spread and rhizomes could trap particles, leading to increased stabilisation of ground away from water.

Roots

Vascular plants evolved true roots made of vascular tissues. Compared with rhizoid, roots can absorb more water and minerals from the soil.

Water delivery is the key to survival. For plants this is through the roots, which need support. The further the roots can grow, the more available water and nutrients. The roots of seed plants became increasingly different from the other plant cells, the stem and leaves.

How did roots push through the hard sediments and gain nutrients? Roots could grow better after flooding, fungi grew with the roots, extending the reach of the roots. In exchange for the energy, the fungi provided minerals to the plants. Bacteria would also have been around, as they can live off hydrogen and oxygen. They didn’t need organic matter in the first instance, but once it was around, they would have soon made use of exudates – glomalin - from the roots.

Rooting would have stopped erosion, in the same way that the spore plants did. Previously any mineral erosion from rocks would have gone straight the water. Now they could be held by the roots, thereby providing means for further growth. (What would have been the necessary minerals then?) Slowing water movement was crucial for development of stable and a soil environment. soils.

Exudates

Root exudates contain a wide variety of molecules released by the plant into the soil. They act as a signalling messenger that allows for communication between soil microbes and plant roots and probably fungi too. Exudates influence several factors within the soil such as nutrient availability, soil pH, and recruitment of bacteria and fungi. The nature of microbial populations around roots are related to root exudates. These fluctuating populations constitute part of what we term the rhizosphere effect, this effect diminishing with increasing distance from the root surface.

Exudates provide food for microbes. We’ll hear a lot about mycorrhiza, but saprotrophic (consuming dead matter) fungi also important. They may not be symbionts, but help distribute exudates and dead plant matter for microbe food and thus help build the rhizosphere/rhizosheath that make up the surrounding atmosphere. This rhizosheath protects plants against pathogens (Christine Jones). 

The four-way symbiotic relationship, between roots, fungi bacteria and small soil animals has been phenomenally resilient, started at this time and surviving for hundreds of millions of years, and perhaps now more important than ever. For more see Glomalisation

Rhizosphere

You can hear about the interplay plant root holobionts, often called the rhizosheath. (Christine Jones) 

It is only in the last 10-20 years that we are recognising the value of this rhizosheath. Lift any plant and the roots should have little lumps of soil sticking to it, so showing that there is a mix of microbes that build the soil particles.

The gene repertoires of mycorrhiza, see next, are amongst the largest in Fungi (> 25 000 genes), but AMF  have lost several genes involved in major metabolic activities, including degradation of lignocellulose yet contain a striking overrepresentation of proteins predicted to play a role in signalling pathways. These genes could facilitate their adaptation to fluctuating environments and different plant hosts. They produce dozens of mycorrhiza-induced small secreted proteins which probably control plant immunity and development during the establishment of the symbiosis.

We are hear more about microbes in soils. But you can be forgiven if that appears to you like the soil is a ‘mush of microbes. We will see through the millions of years that microbes seem to work a lot better if they are in the body of something, whether plant roots or animal guts.

Only in this century have we looked closely at the relations between bacteria and mycorrhizal fungi which we will meet shortly. What we need to remember as we go through the next 400 million years is that the bacterial role is very often very intimate with plants, often being inside their cells. ‘There is a general term ‘Mycorrhiza helper bacteria’ (MHB) This concept has been revisited, and a distinction made between the helper bacteria, which assist mycorrhiza formation and those that interact positively with the functioning of the symbiosis (Frey-Klett et al 2007)

“Our understanding of rhizosphere interactions will remain incomplete without considering their interactions with rhizosphere bacteria, protozoa and plant roots within the heterogeneous pore network of the soil matrix. Rhizosphere interactions are anything but co-operative and unidirectional; rather conflicting interests and reciprocal manipulations to increase own benefits seem commonplace” (Bonkawski 2004)

Plants and their assorted  microbes form a single unit called a 'holobiont', a term used to describe a biological entity that consists of a host organism and all of its associated symbiotic microorganisms and the entire community of organisms that live within and on it, including bacteria, fungi, animals and viruses.

Holobiont

The concept of the holobiont emphasizes the idea that many organisms are not just single individuals, but rather are complex ecosystems made up of multiple species working together in a highly integrated and interdependent manner.


The study of holobionts has become increasingly important in recent years, as researchers have begun to recognize the crucial role that microbiota play in many aspects of host biology, from digestion and metabolism to immune system function and even behaviour. By studying holobionts, scientists hope to gain a deeper understanding of the complex interplay between hosts and their associated microbial communities, and to develop new approaches to promoting health and preventing disease in both humans and other animals.

AMF & Bacteria

While there are now many studies concerning interactions between AM fungi and bacteria, the underlying mechanisms behind these associations are in general not very well understood, and their functional properties still require further experimental confirmation.  Most plant roots are colonized by mycorrhizal fungi and their presence also generally stimulates plant growth. However, the beneficial traits of root-colonizing bacteria and fungi have been mainly studied separately. Only recently have the synergistic effects of bacteria and mycorrhizal fungi been studied with respect to their combined beneficial impacts on plants.” Some bacteria have been shown to directly affect AM fungal germination and growth rate” (Artursson et al 20) 

Bacteria in the rhizosphere

Bacteria play a major role in the rhizosphere arising at this time, as they evolve so fast:

  • Bacteria are key players in breaking down organic matter and releasing nutrients like nitrogen, phosphorus, and potassium, called nutrient recycling so making them available for plant uptake.

  • Certain bacteria, like Rhizobium spp., form symbiotic relationships with leguminous plants. But were they around at this time - as legumes only appeared for 400 million years later. There was Azotobacter, a free-living nitrogen-fixing bacteria in soil then.

Evolution

We saw that bacteria evolved over half billion years ago to trap nitrogen and solubise phosphates in surface films. Now bacteria are relating with the new plant roots.

One study showed that Pseudomonassp which was initially antagonistic to plants can rapidly evolve into being friendly to plants within a few plant generations.(Li et al 2021) Bacteria – because of numbers and speed of growth are able to change quickly – in evolutionary terms.

Other beneficial effects include the nutrients released from consumed bacterial biomass, that is, the ‘microbial loop’. In recent years we have come to recognise bacterial communication networks around the root area (rhizosphere).

"The rhizosphere is generally dominated by Gram-negative bacteria and mycorrhizal fungi, which differ considerably in their ecology (e.g., different metabolic requirements and preferences) from Gram-positive bacteria or saprotrophic fungi". (Balsar 2005)

Hormones

In addition to their properties of capturing nitrogen, solubising phosphates, and helping build aggregates, other bacteria help to produce plant hormones such as auxins, and are known as plant-growth promoting rhizobacteria (PGPR). It is clear the relation between bacteria and plants will have played an important role of the co-development of plants and soil in the early days.It seems that auxins and Cytokinins emerged early in the algal ancestors, while gibberellins came later in the bryophytes (Wang, et al., 2015)

PGPRs

Plant growth promoting rhizobacteria (PGPRs)influence plant growth and development by the production of phytohormones such as auxins, gibberellins, and cytokinins.”Little is known on the genetic basis and signal transduction components that mediate the beneficial effects of PGPRs in plants.” (Ortiz-Castro, Valencia-Cantero, and Lopez-Bucio, 2008).

Plant growth and development are critically influenced by unpredictable changes in their environments, so plants have had to develop robust adaptive mechanisms. Dynamic auxin and cytokinin pathways regulate a plethora of developmental processes, and their crosstalk mediates stress responses, along with other crucial signalling molecules, called reactive oxygen species (ROS) (Bielach, Hrtyan, and Tognetti, 2017)

  • Some bacteria produce growth-promoting substances such as hormones (like auxins) and siderophores (which aid in iron uptake), enhancing plant growth and development.

  • Certain bacteria can suppress soil-borne pathogens through competition for resources, production of antibiotics, or inducing systemic resistance in plants.

Auxins

Bacteria, now found in rhizosphere in wetlands, “have also been reported to produce plant hormones such as IAA, the most common plant hormone of the class of auxins. IAA is responsible for the division, expansion and differentiation of plant cells and tissues and also stimulates root elongation” (Nacoon et al., 2020). Presumably this did not happen until there were roots ie now.

Cytokinins

Cytokinins influence many processes like growth, nutrient responses and the response to biotic and abiotic stresses. Cytokinins are an example of the importance of the vascular system, as they are transported from roots to shoots via the xylem and from shoots to roots via the phloem. The cytokinin signal transduction pathway is similar to that found in bacterial two-component signalling systems, which bacteria sense and respond to environmental stimuli (Kierber and Eric Schaller, 2018)

The phytohormone cytokinin plays diverse roles in plant development, influencing many processes like growth, nutrient responses and the response to biotic and abiotic stresses. Cytokinin levels in plants are regulated by biosynthesis and inactivation pathways. Cytokinins are picked up by receptors that activate a family of transcription factors in the nucleus. Cytokinins are transported from roots to shoots via the xylem and from shoots to roots via the phloem. The cytokinin signal pathway involves a ‘phosphorelay’ similar to that in bacterial signalling systems, used to sense and respond to environmental stimuli (Kierber and Eric Schaller, 2018). The two key components in these bacterial signalling systems are a sensor in their membrane that picks up environmental stimuli, and a response that propagates the signal often directly copying the target genes. Despite the enormous progress made in understanding cytokinin metabolism and signalling, important questions remain.

  • They are also involved in signalling in ways we are just exploring, see cytokinins and TIR signalling, below.

  • They can degrade or detoxify various pollutants, helping to improve soil quality and mitigate environmental contamination. But then that was not a problem like today.

TIR signalling

TIR is a protein domain, a sort of enzyme that helps in internal sigmalling. (Jacob et all 2022). They are made of around 150 amino acids, that helps in the defence of most organisms again various attacks. The first TIR domain protein architecture is present in prokaryotes, oomycetes, plants, and animals (Lapin et al., 2022). Certain TIRs are present in multiple land plants including bryophytes, indicating they have been conserved for over 500 my. Plant TIR-based signalling is emerging as central to the potentiation and effectiveness of host defences. Equally relevant for plant fitness are mechanisms that limit potent TIR signalling in healthy tissues but maintain their preparedness for infection (Lapin et al., 2022). Increased knowledge of how plants fine-tune their stress pathways in nature is now of fundamental interest in improving crop performance.

The big development at this time is the early formation of roots, albeit quite shallow. Nevertheless they protected a whole new community of organisms, and these realtions have intractable over hundreds of millions of years

Next Plants
360-300mya

Mycorrhiza
Springtails
Spiders
Worms
Other animals

This site is set up by Dr Charlie Clutterbuck
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