Tag Archives: Bacteria

Girl and boy flowers support different microbe communities.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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

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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.

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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.

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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.

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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.

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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

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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).

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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).

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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.

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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).

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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.

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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.

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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.