Information

How does species diversity vs Earth total biomass relate?


Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth?

While there is a lot of esoteric sort of talk "humanity dis-balances the live on the Earth", I thought, there are formally seen the following hard facts (correct me if I am wrong):

  • biomass of human species and species we need (plants/cattle etc) is increasing;

  • diversity of species is decreasing

So it looks like some sort of global system change (correct me if I am wrong), but how does biology science discuss them (in case my inquiry can be anyhow scientifically formulated)?


I don't work in ecology, but my first thought is that I would not expect any relationship whatsoever between diversity and biomass. Biomass simply means the combined mass of all life on the planet. If that mass consists of one extremely fat goat the size of the moon, or several trillion different organisms doesn't make a difference, mass is mass.

Now, it is undoubtedly true that loss of diversity is a huge issue. However, the way this works is usually that we replace the local ecosystem with its several, varied species with a monoculture. For example, grasses like wheat and barley are taking over the world. Destroying a forest to plant wheat might easily result in no net change in biomass or even a net positive, but it will certainly be a significant loss in the diversity of the local ecosystem.

Finally, humans are a teeny tiny part of the world's biomass, most of which consists of unicellular life, plants and insects:

Note that the axes in the image above are logarithmic. You can get a clearer image, perhaps, from this:

(both images taken from Bar-On YM, Phillips R, Milo R., The biomass distribution on Earth, PNAS, 2018 Jun 19;115(25):6506-6511. https://www.pnas.org/content/115/25/6506)

See how all animals, let alone humans, are just a tiny part of the image on the right? That gives you a pretty clear indication of just how irrelevant we are in terms of global biomass. So yes, diversity is indeed decreasing, but there is no reason to think that the accumulated mass of living organisms will decrease, only the diversity of said mass will decrease.


Niche Partitioning

Most resource partitioning arguments proposed to explain species diversity assume that the environment is heterogeneous. Coexistence is possible because species have different resource requirements and are specialized to succeed on particular patch types. Diversity is maintained through the presence of an array of patch types. As our ability to measure and quantify environmental variation has improved, we have developed clear evidence that the environment is heterogeneous with regard to resources that are critical to plants. To date, however, we have not critically assessed if the degree of heterogeneity recorded by our instruments is representative of the resource environment perceived by the plants themselves ( Bazzaz, 1996 ). Despite this uncertainty, there is now clear evidence that, at least on the broad scale, species do partition themselves along resource axes. Studies that relate species' distributions to multiple environmental factors using either direct or indirect gradient analysis have identified numerous soil-related axes of specialization, e.g., R. H. Whittaker's 1956 work on the vegetation of the Great Smoky Mountains. Research on experimentally produced plant communities also supports the notion that species may be differentiated along soil resource axes (see studies discussed in Bazzaz, 1996 ).

Although plants themselves can influence their local environment and thus produce intrinsic heterogeneity within the community, much spatial resource heterogeneity is generated by extrinsic factors, the most common of which is disturbance. In fact, disturbance is judged both by change in availability of resources and by perception of that change. Disturbance events create heterogeneity in resource availability at multiple spatial and temporal scales, and these different scales can allow species to partition the environment in more ways. Awareness of the importance of disturbance events for understanding the maintenance of plant species diversity was heightened when Peter Grubb (1977) proposed that regeneration traits of species should provide a critical axis for differentiation, the so-called regeneration niche. Much of the research on partitioning along this regeneration axis has focused on the broad-scale effects of canopy disturbance, addressing differences in conditions and plant responses between gaps and closed forest. Gap creation generates variability in the light environment and has been advanced as a major factor in increasing diversity at the stand level. Broad guilds of plant species that respond similarly to gap formation (light demanding vs shade tolerant) have been identified in numerous forest communities where vertical canopy stratification creates a wide range of light microenvironments ( Whitmore, 1989 ). More recently, sophisticated mathematical techniques have been used to classify both physiological and demographic responses of tree seedlings to light availability more precisely (see SORTIE papers of Steve Pacala, Richard Kobe, and others). Much of this research into species' responses to total light quantity has found considerable overlap in response, and species' partitioning of the light microenvironment is not usually sufficient to explain maintenance of species diversity, particular in communities with high numbers of co-occurring species, such as lowland tropical rain forest.

An additional mechanism for the maintenance of diversity arose from the gap partitioning hypothesis, originally developed by Ricklefs (1977) and applied specifically to the tropical rain forest by Julie Denslow (1980) . Here, finer-scale variation in resource availability across the gap–understory continuum was suggested as a possible mechanism for coexistence in multispecies communities. Unfortunately, this hypothesis has yet not been validated in tropical rain forests, where we lack a good understanding of the maintenance of species diversity. Experimental work by Tim Sipe and F. A. Bazzaz in temperate forests in eastern North America, in contrast, provides some support for the gap partitioning hypothesis. In experimentally created gaps at Harvard Forest in central Massachusetts, we found clear micro-environmental differences between gaps of different sizes (especially with regard to light). We compared morphological and physiological responses of three co-occurring maple (Acer) species to this light variation and found clear evidence that the species differed in their response to gap size. Many response variables showed significant differences between large gaps, small gaps, and understory plots, and these differences often varied between species, creating distinct species' preferences for canopy gap environment ( Fig. 4 ). We also observed substantial variation in light availability between different parts of canopy gaps, due to seasonal and diurnal trends in solar patterns. This variation, however, was rarely reflected in differences in species' responses to position within the gap.

Figure 4 . Survival (a) and growth (b) responses of striped maple (Acer pensylvanicum, triangles), red maple (Acer rubrum, circles), and sugar maple (Acer saccharum, squares) seedlings to canopy gap size. Data redrawn from Sipe and Bazzaz (1994), Ecology 75, 2318–2332, and Sipe and Bazzaz (1995), Ecology 76, 1587–1602.


6: Species Diversity

  • Contributed by Nora Bynum
  • Instructor and Vice Provost for Duke Kunshan University (Environmental Science & Policy Division) at Duke University

Strictly speaking, species diversity is the number of different species in a particular area (species richness) weighted by some measure of abundance such as number of individuals or biomass. However, it is common for conservation biologists to speak of species diversity even when they are actually referring to species richness.

Another measure of species diversity is the species evenness, which is the relative abundance with which each species is represented in an area. An ecosystem where all the species are represented by the same number of individuals has high species evenness. An ecosystem where some species are represented by many individuals, and other species are represented by very few individuals has a low species evenness. Table shows the abundance of species (number of individuals per hectare) in three ecosystems and gives the measures of species richness (S), evenness (E), and the Shannon diversity index (H).

  • (&rho_i) is the proportion of the total number of specimens ii expressed as a proportion of the total number of species for all species in the ecosystem. The product of (&rho_iln(&rho_i)) for each species in the ecosystem is summed, and multiplied by (&minus1) to give (H). The species evenness index ((E)) is calculated as (E=frac<>>).
  • (H_) is the maximum possible value of (H), and is equivalent to (ln(S)). Thus (E=frac)

See Gibbs et al., 1998: p157 and Beals et al. (2000) for discussion and examples. Magurran (1988) also gives discussion of the methods of quantifying diversity.

In Table, ecosystem A shows the greatest diversity in terms of species richness. However, ecosystem B could be described as being richer insofar as most species present are more evenly represented by numbers of individuals thus the species evenness (E) value is larger. This example also illustrates a condition that is often seen in tropical ecosystems, where disturbance of the ecosystem causes uncommon species to become even less common, and common species to become even more common. Disturbance of ecosystem B may produce ecosystem C, where the uncommon species 3 has become less common, and the relatively common species 1 has become more common. There may even be an increase in the number of species in some disturbed ecosystems but, as noted above, this may occur with a concomitant reduction in the abundance of individuals or local extinction of the rarer species.

Species richness and species evenness are probably the most frequently used measures of the total biodiversity of a region. Species diversity is also described in terms of the phylogenetic diversity, or evolutionary relatedness, of the species present in an area. For example, some areas may be rich in closely related taxa, having evolved from a common ancestor that was also found in that same area, whereas other areas may have an array of less closely related species descended from different ancestors (see further comments in the section on Species diversity as a surrogate for global biodiversity).

To count the number of species, we must define what constitutes a species. There are several competing theories, or "species concepts" (Mayden, 1997). The most widely accepted are the morphological species concept, the biological species concept, and the phylogenetic species concept.

Although the morphological species concept (MSC) is largely outdated as a theoretical definition, it is still widely used. According to this concept: species are the smallest groups that are consistently and persistently distinct, and distinguishable by ordinary means. (Cronquist, 1978). In other words, morphological species concept states that "a species is a community, or a number of related communities, whose distinctive morphological characters are, in the opinion of a competent systematist, sufficiently definite to entitle it, or them, to a specific name" (Regan, 1926: 75).

The biological species concept (BSC), as described by Mayr and Ashlock (1991), states that "a species is a group of interbreeding natural populations that is reproductively isolated from other such groups".

According to the phylogenetic species concept (PSC), as defined by Cracraft (1983), a species : "is the smallest diagnosable cluster of individual organism [that is, the cluster of organisms are identifiably distinct from other clusters] within which there is a parental pattern of ancestry and descent". These concepts are not congruent, and considerable debate exists about the advantages and disadvantages of all existing species concepts (for further discussion, see the module on Macroevolution: essentials of systematics and taxonomy).

In practice, systematists usually group specimens together according to shared features (genetic, morphological, physiological). When two or more groups show different sets of shared characters, and the shared characters for each group allow all the members of that group to be distinguished relatively easily and consistently from the members of another group, then the groups are considered different species. This approach relies on the objectivity of the phylogenetic species concept (i.e., the use of intrinsic, shared, characters to define or diagnose a species) and applies it to the practicality of the morphological species concept, in terms of sorting specimens into groups (Kottelat, 1995, 1997).

Despite their differences, all species concepts are based on the understanding that there are parameters that make a species a discrete and identifiable evolutionary entity. If populations of a species become isolated, either through differences in their distribution (i.e., geographic isolation) or through differences in their reproductive biology (i.e., reproductive isolation), they can diverge, ultimately resulting in speciation. During this process, we expect to see distinct populations representing incipient species - species in the process of formation. Some researchers may describe these as subspecies or some other sub-category, according to the species concept used by these researchers. However, it is very difficult to decide when a population is sufficiently different from other populations to merit its ranking as a subspecies. For these reasons, subspecific and infrasubspecific ranks may become extremely subjective decisions of the degree of distinctiveness between groups of organisms (Kottelat, 1997).

An evolutionary significant unit (ESU) is defined, in conservation biology, as a group of organisms that has undergone significant genetic divergence from other groups of the same species. According to Ryder, 1986 identification of ESUs requires the use of natural history information, range and distribution data, and results from analyses of morphometrics, cytogenetics, allozymes and nuclear and mitochondrial DNA. In practice, many ESUs are based on only a subset of these data sources. Nevertheless, it is necessary to compare data from different sources (e.g., analyses of distribution, morphometrics, and DNA) when establishing the status of ESUs. If the ESUs are based on populations that are sympatric or parapatric then it is particularly important to give evidence of significant genetic distance between those populations.

ESUs are important for conservation management because they can be used to identify discrete components of the evolutionary legacy of a species that warrant conservation action. Nevertheless, in evolutionary terms and hence in many systematic studies, species are recognized as the minimum identifiable unit of biodiversity above the level of a single organism (Kottelat, 1997). Thus there is generally more systematic information available for species diversity than for subspecific categories and for ESUs. Consequently, estimates of species diversity are used more frequently as the standard measure of overall biodiversity of a region.

Taxon Taxon Common Name Number of species described* N as percentage of total number of described species*
Bacteria true bacteria 9021 0.5
Archaea archaebacteria 259 0.01
Bryophyta mosses 15000 0.9
Lycopodiophyta clubmosses 1275 0.07
Filicophyta ferns 9500 0.5
Coniferophyta conifers 601 0.03
Magnoliophyta flowering plants 233885 13.4
Fungi fungi 100800 5.8
"Porifera" sponges 10000 0.6
Cnidaria cnidarians 9000 0.5
Rotifera rotifers 1800 0.1
Platyhelminthes flatworms 13780 0.8
Mollusca mollusks 117495 6.7
Annelida annelid worms 14360 0.8
Nematoda nematode worms 20000 1.1
Arachnida arachnids 74445 4.3
Crustacea crustaceans 38839 2.2
Insecta insects 827875 47.4
Echinodermata echinoderms 6000 0.3
Chondrichthyes cartilaginous fishes 846 0.05
Actinopterygii ray-finned bony fishes 23712 1.4
Lissamphibia living amphibians 4975 0.3
Mammalia mammals 4496 0.3
Chelonia living turtles 290 0.02
Squamata lizards and snakes 6850 0.4
Aves birds 9672 0.6
Other 193075 11.0

Table (PageIndex<1>) : Estimated Numbers of Described Species, Based on Lecointre and Guyader (2001) * The total number of described species is assumed to be 1,747,851. This figure, and the numbers of species for taxa are taken from LeCointre and Guyader (2001).


What is the difference between species diversity and species richness?

Species diversity is a measurement of species richness and species evenness. Species richness is the number of species.

Explanation:

Species richness is the number of species found in a community or ecosystem.

Species diversity is a measurement of species richness combined with evenness, meaning it takes into account not only how many species are present but also how evenly distributed the numbers of each species are.

For example, if two communities both have five species, species richness would be five for both communities. If the first community had 100 individuals and 80 of them were all one species, this would not be a community with a very even distribution. If the second community had 100 individuals, with 20 individuals belonging to each of the five species, this community would be more evenly distributed. Because it was more evenly distributed, community two would have a greater species diversity.

In the image below, community one would have a greater species diversity because the spread of species is more even.


Which life form dominates Earth?

Which organism has had the biggest impact on the planet?

We humans tend to assume we rule the Earth. With our advanced tool making, language, problem solving and social skills, and our top predator status, we like to think of ourselves as the dominant life form on the planet.

There are organisms that are significantly more numerous, cover more of the Earth&rsquos surface and make up more of its living biomass than us. We are certainly having major impacts in most corners of the globe and on its other inhabitants.

But are there are other living things that are quietly having greater, more significant influences? Who or what is really in charge?

If world domination is a numbers game, few can compare with tiny six-legged, shrimp-like springtails, or Collembola. Ranging from 0.25-10mm in length, there are typically around 10,000 per square metre of soil, rising to as many as 200,000 per square metre in some places. The 6,000 known species of these wingless arthropods can be found in all manner of habitats all over the world, from beaches and cliffs to the Antarctic and the highest mountain ranges on Earth.

&ldquoOn tarmac you might need to go down a few inches, but anywhere you go on a land surface I would put money that there are springtails just under your feet,&rdquo says Dr Peter Shaw, a zoologist at the University of Roehampton, UK, and the UK Recorder for Collembola.

Ants control every millimetre of the Earth&rsquos surface

Springtails are so named because those that live on surfaces have a springing organ called a furca on the undersides of their abdomens. Flicking this organ allows them to jump up to 10cm to escape predators. Despite sharing the same name, soil-dwelling springtails don&rsquot have furcas. The group&rsquos defining feature is that they all have a tube on their abdomens that they use to suck up water and from which a sticky substance can be exuded to help them stick to surfaces.

Alongside fungi, springtails speed the recycling of dead plants into reusable nutrients. Their importance in this process varies widely according to habitats and the presence or otherwise of other decomposers such as earthworms. But some estimates suggest they are responsible for up to 20% of litter fall decomposition in some places.

Springtails used to be described as the most abundant insects on Earth. However, DNA analysis carried out around 15 years ago found they are actually relatives of insects.

Ants do pretty well in the numbers game too, with estimates of their global population ranging from 10,000 trillion to a quadrillion (a million trillion). While counting ants is difficult and these estimates could be out by a good few zeros, it&rsquos pretty safe to say ants are the most numerous insects in the world.

Despite being outnumbered by springtails, they have far greater and more varied powers to influence the environments in which they live.

&ldquoAnts control every millimetre of the Earth&rsquos surface wherever they live, which is most places,&rdquo says Mark Moffett, an entomologist at the Smithsonian Institute in Washington DC, US, who in 2011 published a book called Adventures Among Ants. &ldquoThese territories are basically micromanaged by ants, altering or removing things even at a microbial level to their benefit.&rdquo

The biomass of plants on land has been estimated to be around 1,000 times that of animals

Ants exert their control in a wide range of ingenious ways, from moving more earth about than earthworms, clearing away their dead to reduce the spread of disease and waging war. Leaf cutter ants farm fungi as a food source and use a bacterial pesticide related to penicillin to improve the productivity of their farms, while herder ants keep herds of aphids so they can milk them for a sugary substance called honeydew.

Of the 14,000 or so known ant species, the most domineering, aggressive ones are those that are so well adapted that they are capable of moving freely around the world forming giant colonies of billions of individuals, allowing them to take on and beat much bigger enemies.

Beetles are the most dominant, species-rich group of organisms

One such species, the Argentine ant, has spread from its South American origins to every continent except Antarctica. They can grow especially quickly because queens tolerate fertile princesses acting as extra breeders. They deploy brute force of numbers, ruthlessness and advanced war strategies to over-run rivals, other animal species and native plants, and have established super-colonies that stretch up to 6,000km along the coastlines of the Mediterranean, California in the US, and western Japan.

But then perhaps a few large things can dominate lots of small things in less obvious but more fundamental ways.

Leaving aside bacteria, the biomass of plants on land has been estimated to be around 1,000 times that of animals. And while other life forms may be more numerous individually, more obviously assertive or more diverse, the vast majority couldn&rsquot exist without the oxygen that plants supply through photosynthesis.

Angiosperms, or flowering plants, make up around 90% of all plant species. They cover a large proportion of the Earth&rsquos land, account for much more biomass than terrestrial animals and provide the structural canvass of the vast majority of land-based eco-systems.

&ldquoThe way a desert is structured differently to a tropical rainforest or your local park is down to the way flowering plants partition up those particular spaces,&rdquo says Sandy Knapp, Head of Plants, at the Natural History Museum in London, UK. &ldquoThey provide places for insects to go, and the space in which other things evolve and change.&rdquo

Then again, maybe world domination is more a matter of diversity and specialisation.

Scientists have so far named some 400,000 species of beetle, meaning they make up between one in five and one in three of all types of described life form, depending which of the various figures for the total species count you believe. They have become successful by evolving to take on highly specific roles, such as pollinating particular trees or feeding on the dung of specific animals.

Wolbachia are extremely widespread and devious

&ldquoBeetles are the most dominant, species-rich group of organisms in terrestrial eco-systems,&rdquo says Max Barclay, beetle collection manager at the Natural History Museum in London. &ldquoThey have divided the world up into very small pieces to specialise in their different jobs, managing to co-exist without competing with each other.&rdquo

It is not just their adaptability and diversity that gets beetles on the shortlist. They also have pivotal roles in most eco-systems, releasing nutrients that are then available to other life forms, by breaking down wood and dung, for example. If insects - of which 40% of species are beetles - were not about, for example, most plants would not get pollinated and so would not be about to generate oxygen.

Weevils are a particularly good example of the importance, and some would say dominance, of beetles.

With their mouths on the ends of long snouts, they can drill holes in plants, into which they deposit their eggs through a special ovipositor, or egg-laying tube. This protects their larvae and gives them a separate food source from adults so they are not in competition. They are tightly associated with specific plants, giving them especially important roles within eco-systems. With some 60,000 species in a number of families, they are also highly diverse and specialised, even for a family of beetles.

So far so human-centric. Were he alive today and reading this article, the American scientist and popular science author Stephen Jay Gould would probably protest that we have so far missed a form of life that has proved even more adaptable, is indestructible and astonishingly diverse.

We are living, wrote Gould, in the Age of Bacteria.

Wolbachia provide a particularly good example of the below-the-radar dominance of bacteria. Extremely widespread and devious, they live within the cells of around two-thirds of insects and other arthropods, such as spiders and mites. They can pass between species.

However their main method of transmission is through the eggs of host females.

Nothing competes with them in terms of their dominance

And they exert their dominance by messing with the reproduction of almost every animal they infect, causing some species to change sex, killing off males, and altering their sperm. In doing so, they have in turn affected the survival and evolution of thousands of other species.

Usually parasitic, their extraordinary range of ways to manipulate their hosts, usually to favour females over males for their advantage, has led some scientists to dub them the &ldquoHerod Bug&rdquo, after the biblical king with the blood of thousands of male children on his hands.

For starters some Wolbachia can induce changes to turn male butterflies, woodlice and crustaceans into females, thereby doubling their chances of being passed on. For the same reason, they can also trigger chromosome changes that allow females of some bees, wasps and ants to make clones of themselves, reproducing without the need for males, and fertilisation by sperm.

Then there are their male-killing abilities. Research by Greg Hurst, Professor of Evolutionary Biology at the University of Liverpool, UK, has established that Wolbachia can trigger the death of some male ladybird and butterfly embryos in species in which there is strong competition for resources among young siblings. The females become stronger, and by eating their dead brothers they are better able to help spread the bacteria.

Wolbachia has yet another cunning ability &ndash it can modify the sperm of infected males. This means an infected male mosquito, for example, can only have viable offspring if it mates with a female infected with the same Wolbachia strain.

Cyanobacteria are the most important and successful microorganisms on Earth

On top of this, insects and other arthropods can pick up genes from the bacteria, potentially speeding up the process of the emergence of new species, through lateral gene transfer.

&ldquoWolbachia can, from the way they manipulate and alter their hosts, be drivers of evolutionary change in many species,&rdquo says John Werren, Professor of Biology at Rochester University, New York, US.

Their presence in so many insects and other arthropods, and their abilities to manipulate their hosts to their advantage, in ways that may have created many thousands of new species, makes Wolbachia are a leading candidate for the world&rsquos most dominant life-form.

&ldquoI&rsquom fairly comfortable in saying as far as intracellular bacteria go, and as far as terrestrial bacteria go, nothing competes with them in terms of their dominance,&rdquo adds Werren.

But of course there is more to the Earth than what takes place on land. And not everything that makes oxygen is a plant.

In fact, before cyanobacteria evolved as the first photosynthetic organisms over 2.5 billion years ago, the atmosphere contained very little oxygen. This change to an oxygen-rich atmosphere laid the foundations for the biodiversity we see on Earth today.

If you look up and down the sizes of living things, microbes dominate their scale, humans dominate their scale, ants tend to dominate things in between

Cyanobacteria form motile strings of cells that can break away from their colonies to form new ones. They can be found in almost all aquatic and terrestrial habitats, living within lichens, plants and animals, as well as forming giant visible blue-green blooms in the oceans.

Apart from generating oxygen, their other pivotal role comes from their ability to convert atmospheric nitrogen into organic nitrate or ammonia, which plants need to get from soil to grow.

These roles in nitrogen fixing and early photosynthesis, as well as their ubiquity across habitats, have led scientists such as Ian Stewart of the University of Queensland, Australia, and Ian Falconer of the University of Adelaide, Australia, to argue that cyanobacteria such as trichodesmium are the most important and successful microorganisms on Earth.

Even this cursory look at a handful of life forms from disparate corners of the tree of life reveals that it is easier to talk about organisms being more dominant or having greater impacts at different physical scales.

&ldquoIf you look up and down the sizes of living things, microbes dominate their scale, humans dominate their scale, ants tend to dominate things in between,&rdquo says Moffett.

Beyond counting individual numbers, weight and surface area cover, the definition of dominance as impact on other life forms and their environment varies according to the priorities of those defining the terms. &ldquoHow good a given measure is depends on what question you&rsquore asking,&rdquo says Knapp.

Ants may look pretty dominant if they have just wrecked or destroyed your crops, for example, but they wouldn&rsquot get far without the oxygen that plants provide. Plants wouldn&rsquot have been able to colonise land as they did some 470 million years ago without the fungi that help enhance their photosynthetic carbon uptake and make it easier for them to reproduce.

Fungi meanwhile would never have gained their pivotal roles in most of the world&rsquos eco-systems without the many and varied symbiotic relationships they form with animals, plants and microbes.

&ldquoIt&rsquos a little like trying to work out whether a famous soccer player or a basketball player is more dominant,&rdquo says Werren.

While efforts to claim top dog status for any single life form will always founder on questions of definitions, what such discussions surely highlight is the complex interdependency that exists between the millions of different species of life on Earth.

&ldquoAsking which group of organisms is the most important is a bit like asking which of four pillars holding up a house is most important,&rdquo adds Knapp. &ldquoIf you took any of them away the whole thing would fall over.&rdquo


What is Species Richness?

Species richness is the number of different species found in a given ecosystem, region or a particular area. Species richness is the most common type of biodiversity index. It simply counts the number of different kinds of species present in a particular area or the sampling area. The size of the sample should be decided correctly according to the sampling guidelines and should represent a big area or a large population. When the number of species in a particular location is high, this means the sample has higher species richness. When the number of species counted is low, it indicates the low species richness. The number of individuals of each species is not included into species richness. It does not also account for the abundances of the species or their relative abundance distributions

Species richness is an important index when thinking about conservation of a given habitat to decide what level of conservation measures need to be taken.

Figure 01: Different species in a particular location


Primary Productivity

Primary productivity (PP) is defined as the rate of energy or mass storage in organic matter of plants per unit surface area of the earth. In terrestrial ecosystems PP is conventionally divided into two components: 1) gross primary productivity (GPP) is the amount of organic material synthesized by plants per unit ground area per unit time, and 2) net primary productivity (NPP) is the amount of this organic material that remains after respiratory consumption of organic matter by the plants (Ra). All heterotrophic organisms rely on NPP for their food requirements. In forests, Clark et al. (2001) emphasized that a working definition of NPP for actual measurements must be adapted from the formal definition (above) because direct measurements of GPP and Ra are not possible and accounting for a variety of other losses of organic material from plant tissues during a measurement interval also can be challenging. In theory NPP could be quantified as:

Biomass Components

Total aboveground biomass

Total belowground biomass

Total plant biomass

Production Components

g/m 2 -yr (1997)

where ∆B is net change in biomass and M, H, L, and V are losses of organic matter from plant tissues owing to mortality, herbivory, leaching and volatilization, respectively. The reason that we must add loss terms like mortality to ∆B when calculating forest NPP is illustrated by the case where ∆B=0: if live biomass doesn’t change over a time interval during which losses of organic material are occurring, then the plants must have added new organic material to replace those losses. Thus, the loss terms would be equal to this new production. To estimate forest NPP at Hubbard Brook we quantify changes in live tree biomass using the allometric equations (described above) and we estimate the principal loss terms, tree mortality and mortality of ephemeral tissues (leaves and fine roots). Some of the other loss terms in Equation 1 also have been measured at Hubbard Brook. Although H, L and V usually comprise a relatively small proportion of aboveground NPP (ANPP), herbivory can be substantial during rare irruptions of defoliating insects. For example, during the peak year of a 3-yr irruption of a defoliating caterpillar (Heterocampa guttivita) about 44% of leaf tissue was consumed in the hardwood forest at HBEF, with local patches of 100% defoliation (Holmes and Sturges 1975). Finally, loss terms for belowground NPP (BNPP) are notoriously difficult to measure and can comprise a substantial portion of NPP that is particularly sensitive to environmental changes, climate, atmospheric CO2 and soil fertility.

The first estimates of ANPP of the Hubbard Brook forest were calculated in the 1960s by Whittaker et al. (1974). At that time the forest on W6 was about 50 yrs old and ANPP was estimated at 924 g/m 2 -yr. Since that time ANPP has declined considerably Fahey et al. (2005) estimated ANPP of the same forest at age ca. 90 yrs to be 708 g/m 2 -yr (Table 1). Roughly half of this total was associated with increment of woody tissue and half with replacement of ephemeral tissue (mostly foliage). The ANPP of the northern hardwood forest at Hubbard Brook is similar to a variety of other mature Acer-dominated forests worldwide (Table 2).

Belowground production (BNPP) includes the growth of perennial woody roots, the replacement of ephemeral fine roots as well as organic matter allocated to mycorrhizal fungi and other rhizosphere fluxes (e.g. root exudation). Direct observations of fine roots at Hubbard Brook using minirhizotrons indicate that most of the smallest first-and second-order roots have lifespans of about one year while higher order (order 3-4) roots live for several years (Tierney and Fahey 2001). On the basis of these observations fine root (< 1mm) production has been estimated at 182 g/m 2 -yr, considerably lower than the production of aboveground ephemeral tissues (342 g/m 2 yr Table 2). However, total rhizosphere C flux has been estimated to be as high as 160 g/m2-yr (Fahey et al. 2005) so that BNPP may comprise as much as 37% of total forest NPP (Table 1).


Figure 3. Spatial pattern of estimated aboveground net primary productivity across the Hubbard Brook valley for 1990-1995.The interpolations are based on 370 plots for which diameter growth of all trees (> 10 cm DBH) was measured. Error estimates are given in the text. (Fahey et al., 2005).

The spatial pattern of ANPP of the Hubbard Brook forest generally reflects that of biomass (compare Figure 2 vs. 3).

For example, 42% of the variation in woody biomass production is explained by aboveground biomass across the 370 plots represented in Figure 2 and 3. The most notable decoupling between biomass and productivity is for fir-birch-spruce dominated stands at the upper elevations, where the production:biomass ratio is notably higher than elsewhere in the HB valley. The temporal pattern of NPP following large-scale disturbance follows the usual pattern of increase to a peak value after a few decades, followed by decline at greater ages. Such an age-related decline in NPP appears to be virtually universal in all forests (Ryan et al. 1997) and has been attributed to a wide range of causes. These temporal and spatial patterns beg the basic question: what limits NPP in the Hubbard Brook forest?

In general, forest NPP is limited by a variety of environmental conditions (e.g., temperature) and resources. In the cold temperate climate of the Northeast the short growing season during which temperatures are suitable for plant growth (i.e., the frost-free season averages 145 d Bailey et al. 2003) is a fundamental constraint on NPP. Temperature limitations contribute to both temporal and spatial variation in NPP at Hubbard Brook. For example, the time interval between leaf out and senescence for the broadleaf deciduous trees varies by about 30 d across years at HBEF (ca. 125-155 d Bailey et al. 2003), and the range of this index of growing season length across elevation (480-820 m) at Hubbard Brook is about 21 days. According to the simulation model PnET about 25% of annual variation in GPP can be explained by growing season length however, plant respiration also is greater in years with long, warm seasons, so that the effect on NPP is much lower (e.g., only 6% of annual in net photosynthesis is explained by growing season length Figure 4).


Figure 4. The effect of growing season length on simulated primary productivity using the model PnET-II (Aber et al. 1995) parameterized for a northern hardwood forest at the HBEF. Leaf area duration (LAIMo) represents the product of daily estimated forest LAI and monthly time intervals for each year. (Fahey et al., 2005).

Another atmospheric condition that limits forest NPP is atmospheric CO2 concentration as demonstrated in free-air CO2 enrichment (FACE) studies in several forests (Norby et al. 2005). Although FACE experiments have not been conducted at HBEF, we have used the PnET model to evaluate possible effects of rising CO2 on NPP, independent of climate change effects. One key effect of rising atmospheric CO2 concentration on forest physiology is to allow greater stomatal control over water loss. Water-use efficiency (WUE) is defined as the ratio of plant photosynthesis per unit water loss by transpiration. Recent measurements indicate that the WUE of northeastern U.S. forests has risen steadily with atmospheric CO2 over the past two decades (Keenan et al. 2013), probably explaining the unexpected observation that declining actual evapotranspiration from the HB watersheds has accompanied rising temperatures (see Climate Change chapter)

The water-use efficiency result emphasizes that soil resource availability serves as an important constraint on forest NPP. Although precipitation is moderately high at HBEF and evenly distributed through the year, soil moisture deficits and drought stress occur occasionally. The dominant tree species are drought avoiders that close their stomata at relatively high soil water potential, thereby reducing potential damage but restricting photosynthetic C gain (Federer 1977). Notably, regional climate warming, which in the absence of CO2-induced increases in WUE would promote higher water loss by the trees, has been accompanied by increasing annual precipitation (see Climate Change chapter)

The role of soil fertility in limiting NPP of northern hardwood forests has received considerable study over the years. Based on a recent meta-analysis of forest fertilization studies, Vadeboncoeur (2010) concluded that NPP of most young northern hardwood forests (e.g. < 30 yr) responded to the addition of N, P, K or Ca or various combinations, with primary limitation by N being most common. Evidence for nutrient limitation of NPP in mature forests was mixed. Recent results from an ongoing N x P nutrient amendment experiment in and around HBEF suggest that P limitation may be widespread in mature northern hardwood forests.

The effects of natural variation in soil nutrient availability on biomass accumulation and NPP of the Hubbard Brook forest have been modified by inputs of pollutants derived from human activity: acid precipitation and nitrogen deposition. Although direct evidence that N deposition has altered NPP of the mature forest is scant, reduction of NPP owing to depletion of soil base cations by acid deposition has been shown conclusively in the Ca remediation experiment on W1 at HBEF(Battles et al. 2013). As noted earlier, the unexpected plateau in forest biomass on W6 is explained in part by this effect. Specifically, soil Ca depletion has limited biomass accumulation primarily by causing decline of the dominant species, sugar maple, which is particularly sensitive to low soil Ca availability (Long et al. 2009). Crown deterioration and reduced LAI of sugar maple, attributed to soil Ca depletion, has contributed to the relatively low ANPP and biomass accumulation on W6 (Battles et al. 2014). In addition to reduced net photosynthesis owing to LAI loss, higher costs of wound repair and plant defense accompany the impaired Ca nutrition of sugar maple in the reference forest (Huggett et al. 2007 Halman et al. 2015). As detailed by Tominaga et al. (2010), recovery of soil base cation status is expected to be delayed in the immediate future because of the high magnitude of 20 th century losses and continuing acid deposition (albeit at lower levels).


Figure. 5. ANPP for three elevational zones of W2 (open diamond, lower third open square, middle third open triangle, upper third) compared with site averages for conventionally harvested sites (solid squares). (Reiners et al., 2012).

An interesting case study of the development of forest biomass and NPP following large-scale disturbance in northern hardwoods is provided by the deforestation study on W2. Reiners et al. (2012) hypothesized that the extreme disturbance of the deforestation treatment on W2 (see W2 Experimental Summary) would exceed the capacity for forest ecosystem resilience. In particular, the treatment resulted in loss of 28% of the ecosystem stock of total N (as well as smaller proportions of base cations) eliminated vegetative sprouting and advance regeneration as sources of forest regeneration and greatly reduced the abundance of fast-growing pin cherry. Surprisingly, despite an initial lag in biomass accumulation and net primary productivity, the forest on W2 followed a trajectory similar to (though on the low end) of comparable sites that had been harvested by conventional methods (Figure 5).

The slowest growth and biomass accumulation were observed in the upper elevation zone of the watershed where soils are thinner and less fertile (Johnson et al. 2000). These observations illustrate that northern hardwoods forests on moderately fertile soils exhibit strong resilience of productivity. The mechanisms contributing to this high resilience deserve further study but may include biologically-enhanced weathering of primary minerals (Blum et al. 2002), biological nitrogen fixation (Bormann et al. 1993) and enhanced mineralization of relatively stable soil organic matter.


Forest evolution-old growth

As forests get older, conifers and hardwoods take over from the fast growing softwood trees. These trees produce great amounts of shade and don’t allow the sun loving bushes adequate sunshine to be able to grow abundantly. The number of species dwindles to those that can live in limited sunlight. This limits the number of kinds of plants that can survive, cutting down on the number of species that are found.

Likewise, the number of animals, having fewer kinds of plants to eat, become represented by fewer species. If they can’t eat, they can’t survive. For the same reason, predators drop in number and species, because there are fewer prey to feed upon.

This progresses as the forest becomes even older. According to Steve T., retired from the US Forest Service, “We see the lack of diversity in older forests all the time. Though we don’t like seeing a major forest fire that burns everything to the ground, it is helpful. It turns back the clock so new growth has a chance to start again, which means more plant and animal species in the area.”

The US Forest Service, in fact, lets fires burn in many places, partly for this reason. The fires don’t just remove the debris from the forest floor, they allow a new growth forest to form, which encourages diversity.

Again according to Steve T., an old growth forest is likely to have as much as 90% fewer plants and animals that a new growth forest has. People often see this outside forested national parks. In the park, the plant-life is rigorously protected. There is a greater likelihood of seeing more plant and animal species outside of the park, where the same regulations aren’t observed.

This all adds up to older forests being less bio-diverse than newer forests. A forest ages naturally. However, it is a mistake to think that old growth forests harbor more animal or plant species than younger forests, since this has been disproved.


Microbial cellulolytic enzymes: diversity and biotechnology with reference to lignocellulosic biomass degradation

Lignocellulosic biomass is the earth’s most abundant renewable feedstock alternative that comprises of cellulose, hemi-cellulose and lignin. The synergistic action of cellulolytic/xylanolytic enzymes produced by lignocellulolytic micro-organisms such as bacteria, algae and fungi are capable of robust cellulosic biomass deconstruction. Most of the microorganisms dwelling in extreme environmental habitats such as rumen environment, hot/cold springs, deep ocean trenches, acidic/alkaline pH environment have been considered as an attractive producers of hemi/cellulolytic lignocellulolytic and other biotechnological enzymes with enhanced bio-chemical properties essential for industrial bioconversion processes. However, the potential microbial sources of cellulolytic enzymes and the underlying mechanism to achieve this is not fully elucidated. In this review article, first we detail the composition of lignocellulosic biomass. Next, we describe the structure and functions of divergent hydrolytic enzymes (cellulolytic and xylanolytic enzymes) involved in cellulosic biomass degradation. Third, we analyze, outline and unveil the prospective source of microbes encoding exceptionally diverse set of biotechnologically relevant cellulolytic enzymes which are critical to answer the specific ecological question of by whom, where and how cellulosic biomass is degraded in the environment. Finally, this review article features the snapshot about the future developments and perspectives on microbial enzymes, high-throughput techniques and molecular tools that could be exploited to derive those enzymes from the potential sources.

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Author information

These authors contributed equally: Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu.

These authors jointly supervised this work: Kankshita Swaminathan, Daniel S. Rokhsar.

Affiliations

Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA

Therese Mitros, Adam M. Session, Jessen V. Bredeson & Daniel S. Rokhsar

DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA

Therese Mitros, Brandon T. James, Mohammad B. Belaffif, Matthew E. Hudson, Erik J. Sacks, Stephen P. Moose, Kankshita Swaminathan & Daniel S. Rokhsar

U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA

Adam M. Session, Guohong Albert Wu, Shengqiang Shu, Kerrie Barry, Jane Grimwood, Jeremy Schmutz & Daniel S. Rokhsar

HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA

Brandon T. James, Mohammad B. Belaffif, Jane Grimwood, Jeremy Schmutz & Kankshita Swaminathan

Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA

Lindsay V. Clark, Hongxu Dong, Adam Barling, Jessica R. Holmes, Jessica E. Mattick, Siyao Liu, Won Byoung Chae, John A. Juvik, Justin Gifford, Adebosola Oladeinde, Matthew E. Hudson, Erik J. Sacks & Stephen P. Moose

High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA

Lindsay V. Clark & Jessica R. Holmes

Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA

Department of Genetics, Curriculum of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27514, USA

Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK

Kerrie Farrar & Iain S. Donnison

Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland

Katarzyna Głowacka & Stanisław Jeżowski

Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA

Department of Environmental Horticulture, Dankook University, Cheonan, 31116, Republic of Korea

Field Science Center for Northern Biosphere, 10-chōme-3 Kita 11 Jōnishi, Kita-ku, Sapporo, Hokkaido, 060-0811, Japan

Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA

Earlham Institute, Norwich Research Park Innovation Centre, Norwich, NR4 7UZ, UK

Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland

Susanne Barth & Manfred Klaas

Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, D2, Dublin, Ireland

Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032, China

Department of Agronomy, Zhejiang University, Hangzhou, 310058, China

HuaZhi Rice Biotech Company, Changsha, 410125, Hunan, China

Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea

Chang Yeon Yu, Kweon Heo & Ji Hye Yoo

Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea

Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA

Matthew E. Hudson, Erik J. Sacks & Stephen P. Moose

Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan

Chan-Zuckerberg BioHub, 499 Illinois St, San Francisco, CA, 94158, USA

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Contributions

D.S.R., K.S., T.M., S.P.M., and M.E.H. provided project leadership. D.S.R., K.S., T.M., S.P.M., A.M.S., B.T.J., G.A.W., and L.V.C. provided figures and wrote the paper. T.M. and J.V.B. assembled the genome and conducted the comparative genomics analysis. N.H.P. generated the HiC assembly. A.M.S. conducted the repeat and allotetraploidy analysis. B.T.J. and M.B.B. conducted the transcriptomic analysis. G.A.W. analyzed the genetic diversity and introgression patterns. S.S. provided the protein-coding gene annotation. H.D. and S.L. provided genetic map data. AB collected samples and provided the transcriptomic, amino acid, and nitrogen data. J.R.H., A.O., and J.E.M. processed samples and extracted nucleic acids for the project. K.F. and I.S.D. contributed the M. sacchariflorus whole-genome sequencing data. J.Gr., J.S., and K.B. coordinated the genome sequencing. K.G. created the double-haploid line and S.J. provided the line. W.B.C. and J.Gi. generated the mapping populations, and J.A.J. and E.J.S. oversaw the generation of the mapping populations. T.Y. provided Ogi63 and Ogi80 triploid lines. J.D.V., L.V.C., S.B., and E.J.S. contributed to RAD-seq data, and J.D.V. and L.V.C. used these data to call variants. M.K., T.H., L.L., X.J., J.P., C.Y.Y., K.H., J.H.Y., and B.K.G. provided miscanthus germplasm.

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