Girl and boy flowers support different microbe communities.

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

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.

Limpet larvae and their fantastic voyage

As he began his PhD program, Takuya Yahagi was puzzled by some laboratory findings. Juvenile red blood limpets, Shinkailepas myojinensis, seemed to survive and grow extraordinarily well at temperatures between 15-25° C. Adult limpets live in deep sea vent communities, where temperatures generally range between 6-11° C.

limpet photo

Adult Shinkailepas myojinensis.  These are approximately 6 mm in length. Credit: Takuya Yahagi.

Yahagi and his colleagues wondered why limpets are making babies that survive and grow at much higher temperatures than they are likely to experience after hatching.

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Deep sea hydrothermal vent community at 795 meters depth at Myojinsho Caldera in the northwest Pacific. White patches on the rocks are vast communities of chemosynthetic bacteria which are being grazed by purple/pinkish limpets. You can also see the white feathery feeding legs of a barnacle population in the upper portion of the photo. Credit: JAMSTEC

Yahagi reasoned that perhaps, in the natural world, the limpet juveniles live in different (warmer) environments than do their parents. If they migrated closer to the sea surface, their world would be somewhat warmer. But limpet babies are microscopic, so capturing them near the sea surface (and knowing that you had captured them!) is very challenging. Working with three other researchers, Yahagi decided to collect indirect evidence to test the hypothesis that baby limpets migrate to the surface where they feed and grow before returning to the ocean depths.


Larval S. myojinensis limpet 156 days after hatching. sh=shell, f =foot, e=eye, vl=velar lobe.

Initially, the researchers needed to determine what temperatures these growing limpets preferred. With the help of a remotely operated submarine, they collected adult limpets laden with egg capsules, and placed newly hatched larvae into separate containers under different conditions. Some larvae were fed and raised at one of six different temperatures: 5, 10, 15, 20, 25 and 30° C. Other larvae were starved at 5, 15 or 25° C to see how long they survived at different temperatures. If the larvae were migrating upwards to warmer waters, it was important to see how long they could survive until they arrived at the richer food sources near the surface.

Starved larvae survived up to 150 days at the lowest temperature, and for more than three weeks at 25° C, which provided ample time for upward migration (even at very mellow baby limpet swimming speeds). Fed larvae grew much more quickly at warmer temperatures, with best growth at 25° C, and no growth at 5-10° C, which is the approximate temperature at hydrothermal vents.. Larvae initially grew quickly at 30° C, but long term exposure to that temperature killed them.


Growth (shell length) of fed larvae at different temperatures.

These temperature profiles corresponded to temperatures at the sea surface down to about 100 meters, which ranged between 19-28° C. This correspondence supported the hypothesis that juveniles migrated upwards in the water column after hatching. But could Yahagi and his colleagues find any direct evidence for this vertical migration? To answer this question, they video-recorded new hatchlings in a clear plastic bath, and measured how fast these limpets swam, and what direction they preferred. They discovered that new hatchlings constantly swam upward in their test bath, and swimming speed was considerably faster at warmer temperatures.

The sea surface is a wonderful place to find food, because sunlight is abundant, so there are abundant phytoplankton to satisfy even the most voracious juvenile limpets. But sea surfaces also have very strong currents which can whisk juvenile limpets hundreds or thousands of kilometers away. The upshot is that vertical migration and wide dispersal of juveniles by ocean currents can introduce new genes into far-away limpet populations.

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A hot vent animal community at 700 meters depth at Minami-Ensei Knoll in the northwest Pacific. Prevalent groups include lobsters (white), two species of shrimp, mussels and two different limpet species. Credit: JAMSTEC.

Gene flow – the movement of genes from one population to another – has some important genetic impacts. Without gene flow, two populations that are separated from each other can become genetically distinct. But the mixing of genes from long-distance dispersal can prevent this from occurring. The researchers compared 1218 base pairs of the COI gene from 77 adult limpets that were collected from four different sites which were separated, in some cases, by more than 1000 kilometers. In support of the gene flow hypothesis they found no evidence of any genetic differentiation among the four populations.

Yahagi Fig1

Hydrothermal vent fields in the northwest Pacific Ocean.  Black squares are limpet collection sites for this study.  Notice the vast distances separating these populations.

Gene flow requires long distance dispersal, and the adult limpets travel very little along the sea floor. This finding of no genetic differentiation among the geographically separated populations supports the hypothesis that the juveniles migrate upwards, feed on abundant phytoplankton, and are carried to new distant environments. There, they mature and settle into new ocean vent communities where they can feed on the superabundant chemosynthetic bacteria associated with the ocean vents. But we still don’t know how limpets find a new ocean vent community – do they migrate, checking out possible vent habitats, while they are still juveniles and still capable of swimming? Do they have sense organs that pick up environmental cues such as hydrogen sulfide content, water temperature, turbulence or noise from vent emissions, to help them complete their fantastic ocean voyage?

note: the paper that describes this research is from the journal Ecology. The reference is Yahagi, Takuya, Hiromi Kayama Watanabe, Shigeaki Kojima, and Yasunori Kano. 2017. Do larvae from deep‐sea hydrothermal vents disperse in surface waters? Ecology 98: 1524-1534Thanks 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.