Bird-friendly viticulture

August 4, 2021 by fredsingerecology

If you are into wine, the Matorral of central Chile is viticulture heaven. This Mediterranean biome has very warm and dry summers and moderate, rainy winters – ideal conditions for grapes. The Matorral’s natural vegetation is a diverse sclerophyll forest composed of trees and shrubs with hard, short and often spikey leaves. Many of these trees and shrubs are endemic – found in the matorral and nowhere else, as are some of the animals that depend on the vegetation for sustenance, making this region a “biodiversity hotspot”. Humans enjoy its benign climate as well, which is why most of Chile’s population and largest cities occupy this bioregion.

Mattoral ecosystem dominates central Chile. Credit: A. Muñoz-Sáez

Unfortunately, the demands of humans for wine and domiciles can come into conflict with the Matorral’s biological diversity. Much of the natural vegetation has already been cleared and most is privately owned, so there is little potential for setting up large preserves. As a long-time bird enthusiast, Andrés Muñoz-Sáez wondered whether even small pockets of natural vegetation could help maintain the biologically diverse bird community in the region. So he and his colleagues conducted a series of systematic surveys to see whether the presence of remnant natural vegetation in the immediate area, or the presence of a continuous forest nearby, increased bird diversity within a vineyard.

A vineyard in central Chile shrouded by fog and surrounded by a sclerophyll forest. Credit: A. Muñoz-Sáez

The researchers conducted 6 auditory and visual surveys for birds in 2014 at 20 vineyards that differed in the amount of surrounding natural vegetation. They repeated this process early and late in the 2015 breeding season, for a total of 360 surveys. There were three types of surveys: (1) Within the vineyard with no natural vegetation remnants within 250 meters, (2) within remnants within the vineyard, and (3) within native vegetation adjacent to the vineyard. The mean size of a remnant was 0.17 hectares. All told, the researchers recorded 5068 birds belonging to 48 species.

A burrowing owl keeps watch while perched on a vineyard fencepost. Credit: A. Muñoz-Sáez

Both species richness (left graph below) and overall bird abundance (right graph below) were lowest in the vineyards without remnants nearby, and highest in remnants and in the surrounding matorral. Richness and abundance were very similar in remnants compared to the surrounding matorral.

Species richness (mean number of species – left graph) and mean number of birds (right graph) per survey conducted in surrounding matorral (M), remnants within a vineyard (R) and in vineyard with no nearby remnants (V). Error bars are 1 standard error. Horizontal bars with *s above bars indicate statistical differences between treatments. * = P < 0.05. *** = P < 0.001.

From the standpoint of species composition (which species were present), bird communities in vineyards with remnants were more like those found in surrounding matorral than like those in vineyards without remnants. Perhaps most important from the standpoint of conserving biological diversity, the mean number of endemic bird species was greatest in matorral (3.02 endemic birds per survey), intermediate within remnants (1.11) and negligible within the vineyard without remnants nearby (0.03).

Muñoz-Sáez and his colleagues advocate retaining remnant native vegetation within vineyards to provide local habitat for native birds. Their surveys indicated that insectivorous birds were more than six times as likely in remnants than in vineyards far removed from remnants. From the standpoint of providing ecosystem services to humans, insectivorous birds can benefit vineyard production by removing unwanted insect pests. Given that many remnants are in less productive areas such as steep slopes, or along streams, the costs of maintaining and not developing these remnants are relatively minor, while the benefits to the viticulturist and the ecosystem can be substantial.

note: the paper that describes this research is from the journal Conservation Biology. The reference is Muñoz‐Sáez, A., Kitzes, J. and Merenlender, A.M., 2021. Bird‐friendly wine country through diversified vineyards. Conservation Biology, 35(1), pp.274-284. Thanks to the Society for Conservation Biology for allowing me to use figures from the paper. Copyright © 2021 by the Society for Conservation Biology. All rights reserved.

It’s all happening at the ecotone

December 30, 2019 by fredsingerecology

In an effort to make order out of the chaos of existence, scientists often resort to classifying stuff. To make order of the natural world, ecologists classify different regions of the world into distinct biomes – large geographical areas with characteristic groups of organisms adapted to that particular environment. Familiar examples of terrestrial biomes are tropical forests, temperate grasslands and desert, and in the aquatic world examples include open ocean, coral reefs and rivers. But what happens at ecotones, where two or more biomes come together? Research has shown that ecotones can be biodiversity hotspots, as the diverse habitats attract many different species, and may also attract edge specialists – species that are particularly adapted to conditions on the border between the two biomes.

Sara Weinstein collects data at the ocean to land ecotone. Credit: Anand Varma.

Sara Weinstein’s graduate research explored the ecology and transmission of raccoon roundworm, Baylisascaris procyonis, a widespread raccoon parasite that causes severe disease in other animals (including humans). She was dissecting raccoons to study infection patterns and as she describes “it would have been a waste of perfectly good raccoon guts to not also examine the rest of the parasite community.” This examination would allow her to determine whether the generalization that ecotones are biodiversity hotspots for terrestrial and aquatic organisms also applies to the much more murky world of gut parasites.

A raccoon poses next to a culvert. Credit: SB Weinstein.

Working with four other researchers, Weinstein compiled a database of published accounts of gastrointestinal parasites from surveys of 256 raccoon populations. They then used this database to classify parasites as either core or satellite. Core parasites are locally abundant, common over a large region and can occupy a broad ecological niche. Satellite parasites are rare, restricted to a small portion of a region and have narrow ecological niches.

Microphallus sp. – a group of relatively rare satellite trematodes collected from a raccoon gut. Credit: SB Weinstein.

Weinstein and her colleagues found that the data divided raccoon gut parasites into two distinct groups.

Top graph. Parasite frequency across raccoon populations. Most parasite genera were found in less than 10% of the raccoon populations. Dashed line indicates 30% cutoff between satellite and core genera. Bottom graph. Proportion of raccoons infected with each parasite in relation to range-wide prevalence. Larger data points indicate more populations surveyed for a given parasite.

There were eight taxa (genera) that were found in more than 40% of raccoon populations. In contrast there were 51 genera that were found in fewer than 30% of raccoon populations, with the vast majority of these found in fewer than 10% of raccoon populations in the survey (top graph on left). The eight common taxa – core parasites – also tended to be present in more individuals within each population than did the 51 less common genera of satellite parasites (bottom graph on left).

Having defined core and satellite parasites, the researchers then did a thorough analysis of the gut contents of 180 raccoon collected by trappers and animal control agents in Santa Barbara County between 2012 – 2015. They hypothesized that the prevalence of core parasites should not be overly affected by ecotones. In contrast, satellite parasites should increase in ecotones, because ecotones provide unique environmental conditions that would be suitable to some of the less common species in the parasite community.

In Santa Barbara County, Weinstein and her colleagues identified four core parasites and nine satellite parasites within the population, with a mean of 2.24 parasite species per raccoon. Racoons nearer to the marine ecotone harbored more parasite species than did raccoons more distant from the marine ecotone, a result of much greater richness of satellite species (left graph below). The story was very different for the freshwater ecotone. Overall, parasite richness was relatively constant in relation to distance from the freshwater ecotone. There were actually fewer core parasites but more satellite parasites near the freshwater ecotone (right graph below).

Left graph. Total parasite richness (orange line) in relation to distance from shore. Satellites (orange fill) increased in abundance near the shore, while core parasites (maroon line) were steady. Right graph. Total parasite richness in relation to distance from freshwater.

Why did core parasite richness decline near the freshwater ecotone? Weinstein and her colleagues believe that diet may play an important role. For example, the core parasites Atriotaenia procyonis and Physoloptera rara were more common in raccoons far from freshwater, probably because racoons are infected by these two parasites as a result of eating terrestrial (but not aquatic) insect species that are intermediate hosts for these two parasite species. As it turns out, these intermediate insect hosts prefer upland habitats that tend to be located relatively distant from the freshwater ecotone.

Increased abundance of rare parasites at ecotones has important implications for human health. Several emerging infectious diseases, such as lyme disease, yellow fever and Nipoh virus are associated with ecotones. Habitat development by the expanding human population is causing increased habitat fragmentation, creating more ecotones, and potentially increasing the prevalence of these and other, equally unfriendly, parasites.

note: the paper that describes this research is from the journal Ecology. The reference is Weinstein, S. B., J. C. Van Wert, M. Kinsella, V. V. Tkach, and K. D. Lafferty. 2019. Infection at an ecotone: cross-system foraging increases satellite parasites but decreases core parasites in raccoons. Ecology 100(9):e02808. 10.1002/ecy.2808. Thanks to the Ecological Society of America for allowing me to use figures from the paper. Copyright © 2019 by the Ecological Society of America. All rights reserved.

Girl and boy flowers support different microbe communities.

March 25, 2019 by fredsingerecology

Most of us are accustomed to thinking about sexual dimorphism in animals. Male lions have manes, and male deer have antlers and generally larger bodies than female deer. In many species, male birds have more complex sings and more colorful plumage. Perhaps less familiar is that female insects are generally larger than males of the same species. But many of us are unaware that sexual dimorphism exists in some plant species as well.

As a child, Kaoru Tsuji spent considerable time watching insects on plants. Later, as an undergraduate at Kyoto University in Japan, she noticed that larvae of a particular geometrid moth only visited male Eurya japonica plants, but not females. This led to her graduate work on how plant sexes affect herbivorous insects, and later, more broadly, on how plant sexual dimorphism affects other species in the community.

Kaoru Tsuji gazes at female Eurya emarginata plant. Credit: Noriyo Tsuji.

At the 2014 Ecological Society of America meetings, Tsuji heard Tadashi Fukami talk about microbial communities in flower nectar, and realized that she could learn to apply Fukami’s techniques to the microbial communities living within Eurya flowers. After working three months in Tadashi’s lab, Tsuji was now ready to explore whether two plant species, Eurya japonica and Eurya emarginata, host different communities of bacteria and fungi in the flowers of male and female plants.

Male and female flowers of the two study species visited by pollinators. These photos are not to scale; in actuality the male flower is substantially larger. You can get a sense of this by noting that the same insect pollinator, the fly Stomorhina obsoleta, is pictured in figure a and near the top left of figure b.

For both species, male flowers tend to be larger, while female flowers tend to have sweeter nectar. Higher sugar levels will increase the chemical stress experienced by microbial organisms living in the nectar. Because the inside of a microbial cell has a lower sugar concentration (and thus a higher water concentration) than the sugar rich nectar environment, water tends to leave the microbial cell, leading to severe dehydration. Thus Tsuji and Fukami expected to find lower microbial abundance in female flower nectar.

Complicating this situation, animal visitors, such as bees and flies, also influence the microbial community in at least two ways. First, many nectar-colonizing microbes depend on animals to disperse them to new flowers. Second, the interaction of nectar production, water evaporation and consumption by bees and flies can change the concentration of sugar in the nectar. If there are few (or no) animals drinking the nectar, water will evaporate, sugar will remain, and the nectar will become more and more concentrated (sweeter) as more nectar is secreted over time. But if nectar gets consumed, the new secretions will simply replace the old nectar, and sugar levels should be relatively constant. Thus flowers without animal visitors should impose more chemical stress on microorganisms by virtue of being sweeter.

The researchers sampled nectar from 1736 flowers, and grew the nectar microbes on agar plates supplied with nutrients that would support either bacterial or fungal growth. In addition, the researchers also placed small-mesh bags over a subset of these flowers (before they opened), to reduce animal visitation. After five days they counted the number of colonies formed, to estimate microbial abundance. Unfortunately, microbes were rarely found in E. japonica, so most of the data are for E. emarginata flowers only.

Female flowers of Eurya emarginata visited by a fly, Stomorhina obsoleta. Agar plates showing isolated colonies of nectar-colonizing microbes are superimposed. Left and right plates have yeast and bacterial colonies, respecitevly, both isolated from E. emarginata nectar. Credit: Kaoru Tsuji and Yuichiro Kanzaki.

First, as expected, female flowers had higher nectar sugar levels than did male flowers (the Brix value measures sucrose concentration). In addition, putting a fine mesh bag over the buds substantially increased sugar levels in nectar from flowers of both sexes.

Sucrose (Brix) concentration of exposed and bagged E. emarginata flowers of both sexes. For box plots, the dark horizontal bar is the median value, while the box encloses the 25th and 75th percentile.

The proportion of flowers in which fungi and bacteria were detected was much greater in male flowers than in female flowers. In male flowers only, bagging the flowers decreased fungal frequency but not bacteria frequency.

The proportion of exposed and bagged E. emarginata flowers whose nectar, when cultured in the appropriate medium, generated fungal colonies (top graph) and bacterial colonies (bottom graph).

The researchers used colony forming units (CFUs) – the number of viable colonies on the agar plate – as their measure of bacterial abundance.

Abundance of fungi (top) and bacteria (bottom) cultured in agar plates, that were swabbed with nectar derived from exposed and bagged E. emarginata flowers of both sexes. Note that the y-axis is log₁₀ CFUs, so an increase from 3 to 4 (for example) is actually a tenfold increase in number of CFUs.

As expected, fungi were less abundant in female flower nectar than in male flower nectar. In addition, bagging the flowers substantially reduced fungal abundance. Bacteria were also less abundant in female flower nectar than in male flower nectar. Surprisingly, bagging the flowers substantially increased bacterial abundance, despite the increased chemical stress and decreased visitation by animal visitors.

Why did bacterial abundance increase when flowers were bagged? The researchers hypothesize that reduced fungal dispersal from bagging caused competitive release of bacteria from the fungi. Presumably the fungi and bacteria compete for essential resources (such as amino acids) in the nectar. Because the bags reduce fungal abundance, there are fewer fungi to out-compete the bacteria, leading to an increase in bacterial abundance.

The researchers used DNA analysis to characterize which microbial species were found in female vs. male flowers. They discovered major differences in species composition between the sexes. Taken together with the data on frequency and abundance, it is clear that sexual dimorphism in these plants influences microbial communities in significant ways. Tsuji and Fukami suggest that sexual dimorphism in many species may have profound community-wide consequences that researchers are only beginning to understand and uncover.

note: the paper that describes this research is from the journal Ecology. The reference is Tsuji, K. and Fukami, T. (2018), Community‐wide consequences of sexual dimorphism: evidence from nectar microbes in dioecious plants. Ecology, 99: 2476-2484. doi:10.1002/ecy.2494. 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.

Rice fields foster biodiversity

January 11, 2019 by fredsingerecology

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.-photo-by-y.g.-baba.jpg

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.

November 29, 2018 by fredsingerecology

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.

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.

Homing in on the micro range

February 8, 2018 by fredsingerecology

I’ve always been fascinated by geography. As a child, I memorized the heights of mountains, the populations of cities, and the areas encompassed by various states and countries. I can still recite from memory many of these numbers – at least based on the 1960 Rand McNally World Atlas. Part of my fondness for geography is no doubt based on my brain’s ability to recall numbers but very little else.

Most geographic ecologists are fond of numbers, exploring numerical questions such as how many organisms or species are there in a given area, or how large an area does a particular species occupy? They then look for factors that influence the distribution and abundance of species or groups of species. Given that biologists estimate there may be up to 100 million species, geographic ecologists have their work cut out for them.

As it turns out, most geographic ecologists have worked on plants, animals or fungi, while relatively few have worked on bacteria and archaeans (a very diverse group of microorganisms that is ancestral to eukaryotes).

Two petri plates with pigmented Actinobacteria. Credit: Mallory Choudoir.

Until recently, bacteria and archaeans were challenging subjects because they were so small and difficult to tell apart. But now, molecular/microbial biology techniques allow us to distinguish between closely related bacteria based on the sequence of bases (adenine, cytosine, guanine, and uracil) in their ribosomal RNA. Bacteria which are identical in more than 97% of their base sequence are described as being in the same phylotype, which is roughly analogous to being in the same species.

As a postdoctoral researcher working in Noah Fierer’s laboratory with several other researchers, Mallory Choudoir wanted to understand the geographic ecology of microorganisms. To do so, they and their collaborators collected dust samples from the trim above an exterior door at 1065 locations across the United States (USA).

Dr. Val McKenzie collects a dust sample from the top of a door sill. Credit: Dr. Noah Fierer.

The researchers sequenced the ribosomal RNA from each sample to determine the bacterial and archaeal diversity at each location. Overall they identified 74,134 gene sequence phyloypes in these samples – that took some work.

On average, each phylotype was found at 70 sites across the USA, but there was enormous variation. By mapping the phylotypes at each of the 1065 locations, the researchers were able to estimate the range size of each phylotyope. They discovered a highly skewed distribution of range sizes, with most phylotypes having relatively small ranges, while only a very few had large ranges (see the graph below). As it turns out, we observe this pattern when analyzing range sizes of plant and animal species as well.

Mean geographic range (Area of occupancy) for each phylotype in the study. The y-axis (Density) indicates the probability that a given phylotype will occupy a range of a particular size (if you draw a straight line down from the peak to the x-axis, you will note that most phylotypes had an AOO of less than 3000 km²

Taxonomists use the term phylum (plural phyla) to indicate a broad grouping of similar organisms. Just to give you a feel for how broad a phylum is, humans and fish belong to the same phylum. Some microbial phyla had much larger geographic ranges than others. Interestingly, it was not always the case that the phylum with the greatest phylotype diversity had the largest range. For example, phylum Chrenarchaeota had the greatest median geographic range (see the graph below), but ranked only 19 (out of 50 phyla) in number of phylotypes (remember that a phylotype is kind of like a species in this study).

Box plots showing range size distribution for individual phyla. Middle black line within each box is the median value; box edges are the 25th and 75th percentile values (1st and 3rd quartiles). Points are outlier phylotypes. Notice that the y-axis is logarithmic.

With this background, Choudoir and her colleagues were prepared to investigate whether there were any characteristics that might influence how large a range would be occupied by a particular phylotype. We could imagine, for example, that a phylotype able to withstand different types of environments would have a greater geographic range than a phylotype that was limited to living in thermal pools. Similarly, a phylotype that dispersed very effectively might have a greater geographic range than a poor disperser.

The researchers expected that aerobic microorganisms (that use oxygen for their metabolism) would have larger geographic ranges than nonaerobic microorganisms, which are actually poisoned by oxygen. The data below support this prediction quite nicely.

Geographic range size in relation to oxygen tolerance. In this graph, and the graphs below, the points have been jittered to the right and left of their bar for ease of viewing (otherwise even more of the points would be on top of each other).

Some bacterial species form spores that protect them against unfavorable environmental conditions. The researchers expected that spore-forming bacteria would have larger geographic ranges than non-spore-forming bacteria.

Geographic range in relation to spore formation (left graph) and pigmentation (right graph).

Choudoir and her colleagues were surprised to discover exactly the opposite; the spore forming bacteria had, on average, slightly smaller geographic ranges. Choudoir and her colleagues also expected that phylotypes that are protected from harsh UV radiation by pigmentation would have larger geographic ranges than unpigmented phylotypes – this time the data confirmed their expectations.

The researchers identified several other factors associated with range size. For example, bacteria with more guanine and cytosine in their DNA or RNA tend to have larger geographic ranges. Some previous studies have shown that a higher proportion of guanine and cytosine is associated with greater thermal tolerance, which should translate to a greater geographic range. Choudoir and her colleagues also discovered that microorganisms with larger genomes (longer DNA or RNA sequences) also had larger ranges. They reason that larger genomes (thus more genes) should correspond to greater physiological versatility and the ability to survive variable environments.

This study opens up the door to further studies of microbial geographic ecology. Some patterns were expected, while others were surprising and beg for more research. Many of these microorganisms are important medically, ecologically or agriculturally, so there are very good reasons to figure out why they live where they do, and how they get from one place to another.

note: the paper that describes this research is from the journal Ecology. The reference is Choudoir, M. J., Barberán, A., Menninger, H. L., Dunn, R. R. and Fierer, N. (2018), Variation in range size and dispersal capabilities of microbial taxa. Ecology, 99: 322–334. doi:10.1002/ecy.2094. Thanks to the Ecological Society of America for allowing me to use figures from the paper. Copyright © 2017 by the Ecological Society of America. All rights reserved.

Treefall gaps deliver diversity

December 4, 2017 by fredsingerecology

When John Terborgh began research at Cocha Cashu Biological Station in Peru back in 1974, he probably did not expect to still be working there 43 years later, doing research and publishing papers about the astounding species diversity in its tropical floodplain rainforest.

John Terborgh leans against a fallen tree that has created a gap in the forest canopy. Credit: Lisa Davenport.

One contributor to species diversity in tropical forests is treefall gaps, which form when a mature tree falls down, opening up a gap in the overhead canopy. The most obvious change associated with treefall gaps is an increase in light that reaches the canopy floor. In comparison to the closed canopy, treefall gaps may be dryer, warmer, have increased plant transpiration rates, and may host many different species that colonize the new environment.

Small treefall gap in a dense rainforest. Credit: Irina Skinner

While it’s clear that gaps influence the physical environment of the forest floor, it is not clear how a changed physical environment translates to biological diversity of the treefall gap community. Comparing treefall gaps to closed canopy communities, Terborgh and his colleagues explored this relationship.

First the researchers asked whether the seed rain into tree gap communities is different from the seed rain into closed canopy communities. Seed rain describes the types and abundance of seeds that are dispersed into communities. Usually seeds are blown into communities by the wind, or enter attached to the bodies or excrement of animals. Alternatively, some seeds are autochorous – self-dispersing, in some cases aided by a change in fruit shape that causes seeds to be ejected explosively.

To do this analysis Terborgh and his colleagues needed a systematic way to measure seed rain. The researchers set up a regularly-spaced grid of small containers (seed traps) that collected a portion of the seeds that entered the community. They also needed a way to describe whether the canopy was closed, somewhat open, or very open as in a treefall gap. For each seed trap they calculated a canopy cover index (CCI), which measured the amount of vegetation found at different levels directly above the traps. A value of 0 indicated no vegetation (a completely open canopy), while a value of 6 indicated dense vegetation at all levels (a completely closed canopy).

As the graphs below indicate, there were some dramatic differences between gaps and canopies. Note that the x-axis has been log-transformed so CCI = 1 transforms to a log(CCI) = 0, and a CCI = 6 transforms to log(CCI) = 0.778. All four major groups of animal seed dispersers dispersed many more seeds into closed canopy forest than into treefall gaps. The relationship between seed abundance and canopy cover was strikingly linear for primates and small arboreal animals. This makes sense, as these animals tend to sit on trees, and spread seeds either through defecation of already eaten fruit, or by eating fruits and inadvertently spilling some seeds in the process. So very few trees in treefall gaps translates to many fewer seeds in treefall gaps, with most (76%) being blown in by the wind.

The log abundance of potentially viable seeds (PV seeds on y-axes) collected in seed traps in relation to the log (canopy cover index) for six different types of seed dispersal agents/mechanisms.

Terborgh and his colleagues realized that differences in seed dispersal could profoundly influence the number and types of plants that were recruited into the population. Despite the scarcity of animals in tree fall gaps, most of the saplings (79%) that recruited into gaps were animal dispersed, whereas wind-dispersed species made up only 1% of the saplings.

Sapling species diversity was greater under a closed canopy.

Sapling species diversity (measured as log(Fisher’s alpha)) in relation to canopy cover (measured as log (canopy cover index)).

Though species diversity was lower in tree fall gaps in comparison to the closed canopy, species composition (the types of species found there) was very different in treefall gaps. There were many species that recruited only under gaps, and were never found under a closed canopy. Interestingly, there is good evidence that the small treefall gaps in this study recruited a different set of tree species than do larger treefall gaps, which tend to recruit species that do best under conditions of very bright sunlight. Thus the researchers conclude that treefall gaps, small and large, offer a wide range of environmental conditions not found in the closed canopy, that ultimately help to promote astoundingly high tropical forest tree diversity.

note: the paper that describes this research is from the journal Ecology. The reference is Terborgh, J., Huanca Nuñez, N., Alvarez Loayza, P. and Cornejo Valverde, F. (2017), Gaps contribute tree diversity to a tropical floodplain forest. Ecology, 98: 2895–2903. doi:10.1002/ecy.1991. Thanks to the Ecological Society of America for allowing me to use figures from the paper. Copyright © 2017 by the Ecological Society of America. All rights reserved.

Cat and fox: agents of Australian extinctions

November 15, 2017 by fredsingerecology

River restoration responses

November 7, 2017 by fredsingerecology

The Lippe River in Germany has been subjected to many decades of channelization, deepening, floodplain drainage, straightening and consequent shortening, with one result being that the modern Lippe is 20% shorter than it was two centuries ago. Beginning in 1996, conservation managers began reversing this trend by widening the river, raising the level of the river bed, constructing small islands within the river and terminating floodplain drainage operations over a stretch of 3.3 km. As a result of these activities, a small portion of the river looks much like it did 200 years ago.

A section of the Lippe River before (left) and after (right) restoration.

Over a 21-year period, researchers from Arbeitsgemeinschaft Biologischer Umweltschutz have conducted systematic surveys of fish communities at the restored and unrestored sections of the river. Researchers sampled the fish community with electrofishing – inputting a direct electrical current into the river – which causes the fish to swim towards the boat where they are easily collected with nets, identified by species, and returned unharmed into the river. A data set over this length of time in association with a restoration project is very unusual; oftentimes (in part due to funding issues) only one survey is conducted to assess the fish community response to river restoration.

About eight years ago, while a postdoctoral researcher at Senckenberg Research Institute in Frankfurt, Germany, Stephan Stoll was asked to analyze some river restoration outcomes, and, as he describes, “became hooked to the topic.” To evaluate the response of the Lippe River fish community to restoration, a group of researchers headed by Stephanie Höckendorff, a Master’s student with Stoll, first asked a very simple question – how did fish abundance and species richness (the number of fish species) compare in the restored and unrestored regions of the river.

The graph below shows several striking trends. Abundance peaked about 2-3 years after restoration, declined sharply the next year, and recovered in subsequent years to about three times the abundance found in unrestored sections. Importantly, abundance varied extensively year-to-year. For example, if you had done only one survey in 2000, you would have erroneously concluded that restoration had no effect, which is why the researchers emphasize the importance of collecting data over a long stretch of time.

Abundance of fish in restored (Rest-gray curve) and unrestored (Cont-black curve) sections of the Lippe River. The gray vertical bar indicates the start of the restoration project in 1997.

Species richness increased sharply, but did not reach its peak until nine years after restoration. Again, there was extensive year-to-year variation in species richness.

Fish species richness in restored (Rest-gray curve) and unrestored (Cont-black curve) sections of the Lippe River. The gray vertical bar indicates the start of the restoration project in 1997.

Höckendorff and her colleagues were intrigued by this delay in species richness, and turned their attention to understanding what types of species benefited most from the restoration. Their analyses indicated that colonizing species, such as common minnows and three-spined sticklebacks, tended to have short life spans, early female maturity, several spawning events per year and a fusiform body shape – a body that is roughly cylindrical and tapers at both ends. Interestingly, some of the most successful colonizers took quite a long time to get well-established within the community.

Common minnows, Phoxinus phoxinus. Credit: Carlo Morelli (Etrusko25)

The three-spined stickleback, Gasterosteus aculeatus. Credit: Ron Offermans

The restored habitat was highly dynamic, experiencing periodic flooding and the formation of temporary shallow bays and shifting sandbanks. These types of habitats tend to select for minnows, sticklebacks and other opportunistic species that are attracted to periodic disturbances. These opportunistic species were quick to move in, and continued to increase in abundance over time. Importantly, several rare and endangered species also colonized the restored habitat. However, large, deep-bodied, slow maturing and long-lived species did not benefit (at least over the 17 years of the survey), as these types of species are generally favored in less dynamic habitats, which are more stable and uniform.

Overall, these findings demonstrate the benefits of river restoration to the fish communities they harbor. But some species are more likely to benefit than others, and the time-scale over which recolonization occurs is highly variable. Surveys must be repeated over a long time-scale to tell conservation managers whether their restoration efforts are successful, and how they might change their future river restoration efforts.

note: the paper that describes this research is from the journal Conservation Biology. The reference is Höckendorff, S., Tonkin, J. D., Haase, P., Bunzel-Drüke, M., Zimball, O., Scharf, M. and Stoll, S. (2017), Characterizing fish responses to a river restoration over 21 years based on species’ traits. Conservation Biology, 31: 1098–1108. doi:10.1111/cobi.12908. 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.

Biodiversity: it’s who you are

August 19, 2017 by fredsingerecology

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.

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Category Archives: Diversity and stability