Rice fields foster biodiversity

Restoration ecologists want to restore ecosystems that have been damaged or destroyed by human activity.  One approach they use is “rewilding” – which can mean different things to different people.  To some, rewilding involves returning large predators to an ecosystem, thereby reestablishing important ecological linkages.  To others, rewilding requires corridors that link different wild areas, so animals can migrate from one area to another.  One common thread in most concepts of rewilding is that once established, restored ecosystems should be self-sustaining, so that if ecosystems are left to their own devices, ecological linkages and biological diversity can return to pre-human-intervention levels, and remain at those levels in the future.

ardea intermedia (intermediate egret). photo by n. katayama

The intermediate egrit, Ardea intermedia, plucks a fish from a flooded rice field. Credit: N. Katayama.

Chieko Koshida and Naoki Katayama argue that rewilding may not always increase biological diversity.  In some cases, allowing ecosystems to return to their pre-human-intervention state can actually cause biological diversity to decline. Koshida and Katayama were surveying bird diversity in abandoned rice fields, and noticed that bird species distributions were different in long-abandoned rice fields in comparison to still-functioning rice fields.  To follow up on their observations, they surveyed the literature, and found 172 studies that addressed how rice field abandonment in Japan affected species richness (number of species) or abundance.  For the meta-analysis we will be discussing today, an eligible study needed to compare richness and/or abundance for at least two of three management states: (1) cultivated (tilled, flood irrigated, rice planted, and harvested every year), (2) fallow (tilled or mowed once every 1-3 years), and (3) long-abandoned (unmanaged for at least three years).


Three different rice field management states – cultivated, fallow and long-abandoned – showing differences in vegetation and water conditions. Credit: C. Koshida.

Meta-analyses are always challenging, because the data are collected by many researchers, and for a variety of purposes.  For example, some researchers may only be interested in whether invasive species were present, or they may not be interested in how many individuals of a particular species were present. Ultimately 35 studies met Koshida and Katayama’s criteria for their meta-analysis (29 in Japanese and six in English).

Overall, abandoning or fallowing rice fields decreased species richness or abundance to 72% of the value of cultivated rice fields. As you might suspect, these effects were not uniform for different variables or comparisons. Not surprisingly, fish and amphibians declined sharply in abandoned rice fields – much more than other groups of organisms. Abundance declined more sharply in abandoned fields than did species richness.  Several other trends also emerged.  For example, complex landscapes such as yatsuda (forested valleys) and tanada (hilly terraces) were more affected than were simple landscapes.  In addition, wetter abandoned fields were able to maintain biological diversity, while dryer abandoned fields declined in richness and abundance.


The effects of rice field abandonment or fallowing for eight different variables.  Effect size is the ln (Mt/Mc), where Mt = mean species richness or abundance for the treatment, and Mc = mean species richness for the control.  The treated field in all comparisons was the one that was abandoned for the longer time.  A positive effect size means that species richness or abundance  increased in the treated (longer abandoned) field, while a negative effect size means that species richness or abundance declined in the treated field. Numbers in parentheses are number of data sets used for comparisons.

When numerous variables are considered, researchers need to figure out which are most important.  Koshida and Katayama used a statistical approach known as “random forest” to model the impact of different variables on the reduction in biological diversity following abandonment.  This approach generates a variable – the percentage increase in mean square error (%increaseMSE) – which indicates the importance of each variable for the model (we won’t go into how this is done!).  As the graph below shows, soil moisture was the most important variable, which tells us (along with the previous figure above) that abandoned fields that maintained high moisture levels also kept their biological diversity, while those that dried out lost out considerably.  Management state was the second most important variable, as long-abandoned fields lost considerably more biological diversity than did fallow fields.


Importance estimates of each variable (as measured by %increase MSE).  Higher values indicate greater importance.

Unfortunately, only three studies had data on changes in biological diversity over the long-term.  All three of these studies surveyed plant species richness over a 6 – 15 year period, so Koshida and Katayama combined them to explore whether plant species richness recovers following long-term rice field abandonment. Based on these studies, species richness continues to decline over the entire time period.


Plant species richness in relation to time since rice fields were abandoned (based on three studies).

Koshida and Katayama conclude that left to their own devices, some ecosystems, like rice fields, will actually decrease, rather than increase, in biological diversity.  Rice fields are, however, special cases, because they provide alternatives to natural wetlands for many organisms dependent on aquatic/wetland environments (such as the frog below). In this sense, rice fields should be viewed as ecological refuges for these groups of organisms.


Rana porosa porosa (Tokyo Daruma Pond Frog). Credit: Y. G. Baba

These findings also have important management implications.  For example, conservation ecologists can promote biological diversity in abandoned rice fields by mowing and flooding. In addition, managers should pay particular attention to abandoned rice fields with complex structure, as they are particularly good reservoirs of biological diversity, and are likely to lose species if allowed to dry out. Failure to attend to these issues could lead to local extinctions of specialist wetland species and of terrestrial species that live in grasslands surrounding rice fields. Lastly, restoration ecologists working on other types of ecosystems need to carefully consider the effects on biological diversity of allowing those ecosystems to return to their natural state without any human intervention.

note: the paper that describes this research is from the journal Conservation Biology. The reference is Koshida, C. and Katayama, N. (2018), Meta‐analysis of the effects of rice‐field abandonment on biodiversity in Japan. Conservation Biology, 32: 1392-1402. doi:10.1111/cobi.13156. Thanks to the Society for Conservation Biology for allowing me to use figures from the paper. Copyright © 2018 by the Society for Conservation Biology. All rights reserved.

What grows up must go down: plant species richness and soils below.

Almost 20 years ago, Dorota Porazinska was a postdoctoral researcher investigating whether plant diversity influenced the diversity of organisms that lived in the soil below these plants, including bacteria, protists, fungi and nematodes (collectively known as soil biota).  Surprisingly, she and her colleagues discovered no linkages between aboveground and belowground species diversity.  She suspected that two issues were responsible for this lack of linkage. First, the early study lumped related species into functional groups – for example nematodes that eat bacteria, or nematodes that eat fungi.  Lumping simplifies data collection but loses a lot of data because individual species are not distinguished.  Back in those days, identifying species with DNA analysis was time-consuming, expensive, and often impractical. The second issue was that even if aboveground-belowground diversity was linked, it might be difficult to detect.  Ecosystems are very complex, and many belowground species make a living off of legacies of carbon or other nutrients that are the remains of organisms that lived many generations ago.   These legacy organic nutrient pools allow for indirect (and thus more difficult to detect) linkages between aboveground and belowground species.

Porazinska and her colleagues reasoned that if there were aboveground/belowground relationships, they would be easiest to detect in the simplest ecosystems that lacked significant pools of legacy nutrients. They also used molecular techniques that were not readily available for earlier studies to identify distinct species based on DNA analysis. The researchers established 98 1-m radius circular plots at the Niwot Ridge Long Term Ecological Research Site in the Colorado, USA Rocky Mountains. At each plot, they identified and counted each vascular plant, and recorded the presence of moss and lichen.  They also censused soil biota by using a variety of DNA amplification and isolation techniques that allowed them to identify bacteria, archaea, protists, fungi and nematodes to species.

PorazinskaOpening9256 Photo

Field assistant Jarred Huxley surveys plants in a high species richness plot. Credit Dorota L. Porazinska.

As expected in this alpine environment, plant species richness was quite low, averaging only 8 species per plot (range = 0 – 27).  In contrast to what had been found in other ecosystems, high plant diversity was associated with high diversity of soil biota.


Relationship between plant richness (x-axis) and soil biota richness (y-axis) for (A) bacteria, (B) eukaryotes (excluding fungi and nematodes), (C) fungi, and (D) nematodes.  OTUs are operational taxonomic units, which represent organisms with very similar or identical DNA sequences on a marker gene.  For our purposes, they represent distinct species.

Looking at the graphs above, you can see that different groups responded to different degrees; nematodes had the strongest response to increases in plant richness while fungi had the weakest response.  When viewed at a finer level, some groups of soil organisms, including photosynthetic microorganisms such as cyanobacteria and green algae actually decreased, presumably in response to competition with aboveground plants for light and possibly nutrients.

Given the strong relationship between plant species richness and soil biota richness, Porazinska and her colleagues next explored whether high plant richness was associated with soil nutrient levels (nutrient pools).  In general, there was a strong correlation between plant species richness and nutrient pools (see graphs below).  But soil moisture, and the ability of soil to hold moisture were the two most important factors associated with nutrient pools.


Amount (micrograms per gram of soil) of carbon (left graph) and nitrogen (right graph) in relation to plant species richness.

Ecologists studying soil processes can measure the rates at which microorganisms are metabolizing nutrients such as carbon, phosphorus and nitrogen.  The expectation was that if high plant species richness was associated with higher soil biota richness, and larger soil nutrient pools, then the activity of enzymes that metabolize soil nutrients should proportionally increase with these factors.  The researchers found that enzyme activity was very low where plants were absent or rare, and greatest in complex plant communities.  But the most important factors influencing enzyme activity were the amount of organic carbon present within the soil, and the ability of the soil to hold water.


Patchy vegetation at the field site. Credit: Cliffton P. Bueno de Mesquita.

Porazinska and her colleagues hypothesize that the relationship between plant species richness, soil biota richness, nutrient pools, and soil processes such as enzyme activity, exist in most ecosystems, but are obscured by indirect linkages between these different levels.  They hypothesize that these relationships in other ecosystems such as grasslands and forests are difficult to observe.  In these more complex ecosystems, carbon inputs into the soil form large legacy carbon pools. These carbon pools, and the ability of the soil to hold nutrient pools, fundamentally influence the abundance and richness of soil biota. In contrast, in nutrient-poor soils, such as high Rocky Mountain alpine meadows, legacy carbon pools are rare and small. Consequently, plants and soil biota interact more directly, and correlations between plant species diversity and soil biota diversity are much easier to detect.

note: the paper that describes this research is from the journal Ecology. The reference is Porazinska, D. L., Farrer, E. C., Spasojevic, M. J., Bueno de Mesquita, C. P., Sartwell, S. A., Smith, J. G., White, C. T., King, A. J., Suding, K. N. and Schmidt, S. K. (2018), Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem. Ecology, 99: 1942-1952. doi:10.1002/ecy.2420. Thanks to the Ecological Society of America for allowing me to use figures from the paper. Copyright © 2018 by the Ecological Society of America. All rights reserved.


Biodiversity: it’s who you are

It is a massive understatement that ecologists and conservation biologists are profoundly interested in how disturbance affects biological diversity. Humans are disturbing ecosystems by degrading or destroying habitat, by fragmenting habitat into pieces that are too small to sustain populations, by directly overexploiting species for consumption or other purposes, and by introducing non-native species (and there’s more!). Some biologists argue that disturbance has gotten so severe that we need to modify our worldview of ecosystems. They argue, for example, that intact grasslands are so rare that we should stop talking about them as an ecosystem (or biome), but rather should more realistically explore the ecology of different types of croplands, which are, in actuality, primarily disturbed grasslands.

Some types of ecosystems, such as rainforests, have survived human impact more than others, but all have been highly disturbed. So it is fitting that conservation ecologists devote their attentions to understanding how disturbance influences biological diversity. Working in Cameroon in 1998, John Lawton and his colleagues assessed species richness (number of different species) in relation to level of disturbance experienced by eight different animal groups: canopy beetles, flying beetles, butterflies, canopy ants, leaf-litter ants, nematodes, termites, and birds. They discovered that more intense disturbances were associated with a significant reduction in species richness for many of the groups.


Tropical forest in Cameroon. Credit: Earwig via Wikimedia Commons

Nigel Stork worked with Lawton on the original study, and recently reanalyzed the data in the context of changes that have occurred in how conservation biologists view biological diversity. For example, many biologists now argue that conserving biological diversity requires understanding which species are affected by disturbance, rather than the number of species. In addition, not all disturbances have similar impacts on biological diversity. For example, logging with heavy equipment removes trees and compacts soil, while logging with lighter equipment does not compact soil, so the two treatments may have very different impacts. Finally, it may be more informative to group species according to ecosystem function rather than by taxonomic group.


Locations of sampling plots within the Mbalmayo Forest Reserve, Cameroon.  The three blown-up sites had multiple plots with different levels of disturbance, as indicated by the key.

Stork and his colleagues only had data for six of the original eight taxonomic groups. They categorized intensity of disturbance based on how much tree biomass was removed, level of soil compaction, time since disturbance, and tree cover and diversity at time of sampling. This allowed the researchers to assign a disturbance index to each plot, with 0 indicating least disturbed and 1.0 indicating most disturbed. This analysis showed no significant relationship between disturbance and species richness in five of the six taxonomic groups, with only termites declining in richness in response to disturbance.


Species richness in relation to intensity of disturbance for six taxonomic groups considered in the study.

Stork and his colleagues used a slightly different approach to assess the response of species composition (the identity of species that are actually present in the community) to disturbance. They compared each pair of surveyed plots in relation to how different they were in disturbance. Plots with very different levels of disturbance had disturbance dissimilarities close to 1.0, while plots with similar levels of disturbance had disturbance dissimilarities near 0. They then looked at community dissimilarity to explore changes in species composition. Plots with a community dissimilarity near 1.0 had very different species, while plots with a community dissimilarity near 0 had very similar species.

Here’s what they found. For five of six groups, disturbance dissimilarity was associated with significant (solid line) or borderline significant (dashed line) increases in community dissimilarity. So even though the number of species was not affected very much by disturbance (excepting termites), species composition was affected in all groups, with the exception of canopy ants. They conclude that a disturbed forest has very different types of species in it, but not necessarily fewer species.


Community dissimilarity in relation to disturbance dissimilarity. For five taxonomic groups, plots that had the greatest differences in disturbance also had the greatest differences in species composition.

Lastly, this study shows that response to disturbance is related to the functional group – the role that each species plays within the community. For example, beetles showed a strong response to disturbance, but in reality the strong response was only true for the herbivorous beetle functional group. Beetles that ate fungi or were predators or scavengers showed relatively little change in species composition in relation to disturbance.

So what should conservation ecologists do with this information? Given the diversity and intensity of disturbance globally, we need to develop a better understanding of how species and communities respond to global change. Species composition may be a more sensitive indicator of disturbance than is species richness. Functional groups may be more helpful than taxonomic groups in identifying how disturbance influences how ecosystems actually work. Perhaps monitoring particular functional groups can give us insight into how unrelated groups with similar ecology might respond to a world that promises to experience increasing levels of disturbance.

note: I discuss two papers in this blog.  The original is from the journal Nature. The reference is Lawton, J.H., Bignell, D.E., Bolton, B., Bloemers, G.F., Eggleton, P., Hammond, P. M., Hodda, M., Holt, R.D., Larsen, T.B., Mawdsley, N.A., Stork, N.E., Srivastava, D.S., and Watt, A.D. 1998. Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature, 391: 72-76. The second paper that reanalyzes the original data is from the journal Conservation Biology. The reference is Stork, N.E., Srivastava, D.S., Eggleton, P., Hodda, M., Lawson, G., Leakey, R.R.B. and Watt, A.D., 2017. Consistency of effects of tropical‐forest disturbance on species composition and richness relative to use of indicator taxa. Conservation Biology 31 (4): 924-933. Thanks to the Society for Conservation Biology for allowing me to use figures from the paper. Copyright © 2017 by the Society for Conservation Biology. All rights reserved.