A Guide to the Natural History of Freshwater Lake Bacteria

Summary: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.     

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Evolutionary morphological and physiological differences between browsers and grazers contribute to species‐specific digestion efficiency of food resources. Rumen microbial community structure of browsers is supposedly adapted to characteristic nutrient composition of the diet source. If this assumption is correct, domesticated ruminants, or grazers, are poor model animals for assessing the nutritional value of food consumed by browsing game species. In this study, typical spring and summer foods of the European moose (Alces alces) were combined with rumen fluid collected from both dairy cows (Bos taurus) and from moose, with the aim of comparing fermentation efficiency and microbial community composition. The nutritional value of the food resources was characterized by chemical analysis and advanced in vitro measurements. The study also addressed whether or not feed evaluation based on in vitro techniques with cattle rumen fluid as inoculum could be a practical alternative when evaluating the nutritional value of plants consumed by wild browsers. Our results suggest that the fermentation characteristics of moose spring and summer food are partly host‐specific and related to the contribution of the bacterial phyla Firmicutes and Bacteriodetes to the rumen microbial community. Host‐specific adaptations of the ruminal microbial community structure could be explained from the evolutionary adaptations related to feeding habitats and morphophysiological differences between browsers and grazers. However, the observed overall differences in microbial community structure could not be related to ruminal digestion parameters measured in vitro. The in vitro evaluation of digestion efficiency reveals that equal amounts of methane were produced across all feed samples regardless of whether the ruminal fluid was from moose or dairy cow. The results of this study suggested that the nutritional value of browsers' spring and summer food can be predicted using rumen fluid from domesticated grazers as inoculum in in vitro assessments of extent of digestion when excluding samples of the white water lily root, but not of fermentation characteristics as indicated by the proportions of individual fermentation fatty acids to the total of volatile fatty acids.     

Nortriptyline and antipyrine clearance in relation to debrisoquine hydroxylation in man

Eight healthy volunteers with a broad range in their ability to hydroxylate debrisoquine, a metabolic reaction which is under polymorphic genetic control, were given single oral doses of nortriptyline and antipyrine. There was a close correlation between an individual's ability to hydroxylate debrisoquine and nortriptyline (measured as plasma clerance of the drug) (Spearman r_s = 0.83; p = 0.01). This indicates that these two benzylic hydroxylations are controlled by similar if not identical genetic factors. In contrast to nortriptyline the clearance of antipyrine (assessed in saliva) was not positively related to the ability to hydroxylate debrisoquine.     

Fertility in Dairy Cows Managed for Calving Intervals of 12,15 or 18 Months

Effects on reproduction in a total of 135 dairy cows managed for calving intervals of 12, 15 or 18 months (72, 38 and 25 cows respectively) were studied. The cows were of the Swedish Red and White Breed (SRB) and the Swedish Freisian Breed (SLB) and were housed in 2 different herds with 3 different management systems (tied, loose, and tied but milked in a milking parlour; mixed). The cows in one of the herds (48 cows) were assigned for milking either 2 times or 3 times a day. When comparing conception rate at 1st insemination (AI) and the percentage of cows finally pregnant, we found no significant differences between the 3 calving interval groups, however, a tendency for a higher conception rate with a 15 months' interval compared with a 12 months' interval was found in one of the herds (50% vs 41.5%). The percentage of finally pregnant animals varied between 81% and 100%, but this variation was mainly attributed to the herd rather than calving interval group. A significantly higher percentage of cows was treated for anoestrous in the 12-month group than in the 15-month group in one of the herds (28.6% vs. 5.3%). The frequency of ovulations with external heat signs increased with ovulation number up to the 4th ovulation and thereafter remained stable. No significant difference was found in number of AIs required per conception with respect to calving intervals, breeds, or milking frequency groups. However, cows milked 3 times a day had a significantly longer interval from the 1 st AI to conception compared with cows milked 2 times a day (45.8 days vs 17.6 days, p<.01). Cows kept loose exhibited 1st ovulatory oestrous, approximately 2 weeks earlier (55.9 days vs 69.7 days, p<.05) than their herd mates kept tied. In conclusion, our study shows that lengthening the calving interval to 15 or 18 months may have a positive influence on reproduction in terms of less need for treatments of ovarian disorders and higher conception rates. Our results also indicate that milking 3 times a day may have negative effects, and keeping cows in a loose-housing management system may have positive effects on ovarian function. kw|Keywords|k]reproduction; k]extended calving intervals; k]cattle; k]milking frequency     

Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing

Seasonal variation in activity of enzymes involved in polymer degradation, including chitinases, has been observed previously in freshwater environments. However, it is not known whether the seasonal dynamics are due to shifts in the activity of bacteria already present, or shifts in community structure towards emergence or disappearance of chitinolytic organisms. We traced seasonal shifts in the chitinase gene assemblage in a temperate lake and linked these communities to variation in chitinase activity. Chitinase genes from 20 samples collected over a full yearly cycle were characterized by pyrosequencing. Pronounced temporal shifts in composition of the chitinase gene pool (beta diversity) occurred along with distinct shifts in richness (alpha diversity) as well as chitin processing. Changes in the chitinase gene pool correlated mainly with temperature, abundance of crustacean zooplankton and phytoplankton blooms. Also changes in the physical structure of the lake, e.g. stratification and mixing were associated with changes in the chitinolytic community, while differences were minor between surface and suboxic hypolimnetic water. The lake characteristics influencing the chitinolytic community are all linked to changes in organic particles and we suggest that seasonal changes in particle quality and availability foster microbial communities adapted to efficiently degrade them.     

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.     

Detection of N-Terminally Extended Substance P but Not of Substance P in Human Cerebrospinal Fluid: Quantitation with HPLC-Radioimmunoassay

A reversed-phase HPLC system was used to concentrate and separate components of substance P-like immunoreactivity (SP-LI) from human CSF. When CSF was injected and fractions collected, no SP-LI could be detected by radioimmunoassay (RIA) at the retention time of SP or SP-sulfoxide. Instead, SP-LI was detected in later eluting fractions. This SP-LI reacted with two different antisera raised against the C-terminal part of SP, but not with an antiserum against the N-terminal part. A compound with similar properties was also found to be present in neutral extracts of rat dorsal spinal cord. When the late-eluting compound from human CSF was treated with trypsin and rechromatographed on HPLC, an immunoreactive component eluting at the position of SP could be detected with both the C- and N-terminally directed SP antisera. These results suggest that an N-terminally extended form of SP is present in human CSF. Trypsinization also gave two other compounds with affinity for the N- but not the C-terminally directed antisera. This may indicate that N-terminal fragments of SP extended at the N-terminus or SP molecules extended at both the N- and the C-terminus (i.e., preprotachykinins) also are present in human CSF. In 32 CSF samples from depressed patients, SP-LI was determined with a C-terminally directed antiserum with and without prior HPLC separation. SP itself could not be detected, but the late-eluting form of SP-LI could be quantitated in all samples by combined HPLC-RIA. In most samples, there was a relatively good agreement between the SP-LI levels measured with and without HPLC.